Can you expand on that? One of the main use cases for GO is statistical enrichment analyses. Of course, there are definitely problems here, from choice of appropriate way to correct for multiple hypotheses to appropriateness of frequentist vs Bayesian methods (e.g. Ontologizer). Is this what you are getting at?

How do you work with it? Are you writing scripts and sparqQL that query an endpoint, or ser you using an ontologi aware databrowser that can do calculations? Or something completely different?