They are published in the areas that include aviation, cancer, chemistry, computer science, food processing, food safety, genealogy, general medicine, geography, healthcare, manufacturing, mathematics, transportation, and weather. There are, in fact, hundreds of published ontologies.
via technorati.com
This directory from Google on Ontologies are a good starting point.
Here are a couple of papers worth reading:
Guided Tour of Ontology by John F.Sowa