Saturday, October 30, 2010

Algorithm or Model: OpenTox API quiz

Nina (who still does not seem to blog) wrote up this interesting question, triggered by the OpenTox API ontology:
    Given: A publication, describing specific method of property prediction (not a generic machine learning algorithm). An implementation of this publication.
    Example: pKa. This is a decision tree with SMARTS in the nodes. There is a training set, which could be used in validation.
    - Should it be exposed by OpenTox services as ot:Algorithm or ot:Model ?
    - What is the right way to use / extend Blue Obelisk descriptors dictionary to describe this implementation?
    - Would you classify this method as a descriptor calculation or as a predictive model?

I would say, a ot:Model is a ot:Algorithm, just a comlex one.

The question shows one of the virtues of ontologies: they require us to carefully think about what we say. It is almost as like they put the scholar back into science.

On a different note, can we please start making an Open Data pKa database?!?