Introduction to Ontologies from McGuinness
Deborah L. McGuinness, ontology goddess, released Ontologies Come of Age, a chapter to an upcoming book. A relatively gentle introduction, along the way she illustrates the difference between controlled vocabularies and ontologies: the former have implicit is-a relationships and the latter have explicit is-a relationships (e.g. in a taxonomy a Merlot is a narrower term of Red Wine, whereas in an ontology a Merlot is-a Red Wine). Expressing those relationships explicitly helps computers understand what we understand. So it's more like knowledge representation, though it relies on the classification techniques of controlled vocabularies.
She's done hardcore research at Rutgers, AT&T, Lucent, & Stanford and seems to be looking for wider applications of this work via Sandpiper Software.