I’m new to Protege/OWL. I’m from the OO world and I’m wondering are there any guidelines on the difference between using OO modeling and ontology modeling? 

I started with a UML model but then stumbled over Protege/OWL and was very impressed with how much better it was for the model I wanted to build. (BTW, Kudos to the Protege team, what a wonderfully intuitive and well designed tool)

But being an OO person I’m still getting up the learning curve on building and thinking in terms of an ontology not an object model. 

To be specific what I’m NOT looking for are:

1. How to convert/integrate OWL models with Java code or other OO languages
2. How to model software components or systems using OWL

When I’ve searched for "OO and OWL" I find mostly papers that address those issues. 

What I AM interested in (and haven’t found much on) are questions such as:

1. How to tell where the boundaries are for an OWL model. Are there points where it just makes sense to say “that’s a functional or process issue not something that goes into an ontology”
2. How to convert an OO model to an OWL model. Especially functions/methods.
3. How to (or whether to) model process and business logic in an OWL model
4. Other tools to use if/when OWL is not appropriate but you still have some bit of behavior or process logic that you want expressed in the model.