A colleague just pointed me to GoPubMed. This is a search engine over PubMed that organizes the returned results using GeneOntology, an ontology for molecular biology. GoPubMed takes the top abstracts from a standard keyword search, uses a soft alignment to find all the phrases in the results that have a node in GeneOntology, and then shows you the subset of GO that's induced by your query. The ontology subset lets you restrict your search in a sensible way, and get an idea of what's in documents that are fairly far down the ranked list. This looks like a nice service. It makes me wonder if we can do something similar with automatically-generated CS ontologies in Rexa.