I work directly in the life sciences side of it. When the microphone is off, other peoples' interaction with me is basically: "Oh great, we have this data which would be pretty straightforward to store and transmit as JSON, but we have to work with this fucker to turn it into some sort of triple format or something." (Can you tell I don't like my job?)

If you pry beneath the surface the life science ontologies are garbage. Full of subtle errors, disagreement between different ontologies, incorrect changing of namespaces which causes backward incompatibility. You have to have 100% knowledge of the ontology's idiosyncrasies in order to use it with confidence (i.e.: you can't).

Funny you mention StarDog. Semantic web is supposedly this great open data thing that's going to unite the world. Except it's such a miserable community there aren't even any decent non-proprietary tools to satisfactorily fulfill the most basic premises of semantic web, after all these years.