Dear All,

Here is the promised example of a complete nearest neighbor prediction.
It is more complicated than the previous substructure example and
contains:

1. The query compound (http://localhost/compound/InChI=1S/C6H8N2/c7-8-6-4-2-1-3-5-6/h1-5,8H,7H2)
2. A lazar prediction for the query compound (http://localhost/dataset/582/feature/prediction/Hamster%20Carcinogenicity/0), this feature has among other annotations also a confidence value
3. Neighbors of the query compound as features (http://localhost/dataset/582/feature/neighbor/*), these features have (among other annotations) a compound, similarity and a measured activity.
4. Substructures of the query compound (http://localhost/dataset/583/feature/descriptor/*), these are the same type of fminer/bbrc substructures as in the previous substructure dataset example
5. Substructures of the neighbors (in data entries of the neighbor compounds)

In addition to the proposed substructure additions, we would need the following entries in the OpenTox ontology:

To distinguish between different types of features: ot:Neighbor, ot:Substructure, ot:ModelPrediction (ot:MeasuredFeature could be useful for values that come from database searches)
To represent neighbors: ot:measuredFeeature, ot:similarity

The main lesson I have learnt from this exercise was to use feature
annotations to represent anything that is more complex than a single
value and to indicate the presence of such a "complex" feature by a
boolean value in the data entries. This allows us also to represent
multiple occurrences of the same feature without having to modify the
API.

Best regards,
Christoph

PS: Please ignore the entry for ot:dependentVariables -  this has to be
fixed.
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