Music metadata (Musicbrainz, AllMusic, etc...) comes to mind. The data is usually more important than the ontology itself, and the ontology is not really consistent across the entire industry, but it's a somewhat relevant example.
Relevant XKCD: https://xkcd.com/927/
Most of the difficulties are with matching artists and content across different databases, which is a separate issue. The ontology itself is tangential, but one example where it's important (even if it's not a fully / cleanly solved problem).