Ontology Driven data Analysis

Many researchers have come to realize that ontologies will definitelly bridge the gap between databases and analysis algorithms. But how to do that in a level of abstraction that is usefull regardless of the data structure? Data analysis tools often become obsolete and need to be adapted as new significant parameters emerge from the data collection. Ontologies are already being used as effective tools for integrating databases and data mining tools for deriving knowledge. But this often happens at a large scale of data wharehouses, where the bench biologist trying to derive conclusions from their data have little to say in the manner the data analysis is conducted.
Ontology driven analysis tools should be flexible enough to accept entry of new parameters that might, or not, improve the probability of the conclusions.