I've been playing with RDF/semantic web for a time and then today I had a glance with Gene Onotolgy (GO) although I don' have currently any project dealing with expression/clusering/etc... First of all, it seems that GO is stored using the OBO format rather than RDF. At this time I don't know the consequences of this but I imagine that I won't be able to use standard XML/RDF tools (XSL,DOM, Protege, Jena...), can GO handles OWL-like relationships (InverseFunctional, Symetric, Transitive...) ? Anyway is this really useful in GO ? I remember there was a paper published in Nature Genetics titled "Are the current ontologies in biology good ontologies?".
I also started my experience with GO by trying to submit a new term "3' RNA binding" in this ontology to be inserted between GO:0003723 RNA binding and GO:0008143 Poly(A) binding, in order to assign this new term to the Rotavirus Non structural protein 3 (NSP3) wich binds specificaly the 3' end of viral mRNAs. The term was not reviewed yet.
Picture from: The 5' and 3' ends of viral and eukaryotic mRNA synergistically stimulate initiation of protein synthesis (Varani & Allain 2002).