Egon pointed to an interesting blog post about a feature that is available as a an extension to Jena, the semantic web framework available in Bioclipse. It allows to very easily query multiple SPARQL endpoints from a single SPARQL query (using the
SERVICE keyword), and use variable bound from one endpoint when querying the next.
This is very useful in general. I was also thinking of the specific scenario (along the lines we have partly already been thinking) to use multiple Semantic MediaWikis as community maintained databanks, for querying back into Bioclipse. Being able to use multiple MediaWiki installs is very useful because it is hard to incorporate a very efficient access restriction system in MediaWiki (due to the nature of how it works, with template calls and all), so then it is better to be able to have separate wikis for content which needs special restrictions.