1) Indeed, we consider visualization of graph dependencies in OntoMathPro as an important application for learning. Given sufficient coverage of relationships between concepts, it can provide a helpful context for any non-trivial term.
2) No, the ontology was constructed collaboratively and manually from scratch, and Wikipedia was just one of the used resources. BTW, overlapping between the math part of Wikipedia (or DBpedia as we think in terms of Linked Data) and OntoMathPro is saved in the mapping file (https://github.com/CLLKazan/OntoMathPro/blob/master/external...), which was extracted automatically afterwards.
3) Concerning "ElementS of Probability Theory", could you please provide class URI you are talking about? Because I can see only this relevant one: E2406 http://ontomathpro.org/ontology/E2406___599545262.html which has the proper name (without 's').
4) We do allow and have multiple inheritance. Please see E1892 Differential Equation, which is a sub-class of both E1891 Equation and E2688 Element of Differential Equations. I believe there are more subtle examples in the ontology (can't remember exactly for now).
5) About ontology engineering principles, if you are interested in, please peruse our research papers (especially, [2]), in which we elaborate our modeling principles.
6) I can't agree about 'weakness' of the chosen language. OWL 2 is quite expressive to provide non-trivial logical rules and properties. For examples, some of them are already in place: P5 'see also' property is transitive and symmetric. Surely, we can't describe the precise semantics of mathematics (we would have to have a more expressive language than mathematics itself according to Popper's methodology). But we don't need it to build fascinating applications atop of the existing ontology, as our work hopefully shows.
BTW, I'd suggest using our mailing list further to keep these valuable discussions in the proper place: https://groups.google.com/forum/#!forum/ontomathpro
Next, you can submit pull requests in GitHub with suggesting improvements, then we can discuss them there.
No offense to HN, it's just to make our life easier.