To build a rule-based expert system, what tools should be chosen? These two seems to be old tools for building expert system:
* Clip: http://www.clipsrules.net/
* Jess in Java
Are these three below also for the purpose of building expert system, as above two?
* Manchester OWL
* Protege OWL
* Jena API
It seems like the traditional 'expert system' has been outdated, and they are replaced by semantic web/ontology technologies. Can I say OWL and Jena API can achieve same things as a traditional expert system?
Short answer: no.
OWL is a knowledge representation language (and a set of applicable inference rules) - it is a W3C standard available here: https://www.w3.org/TR/owl2-overview/
Jena API supports RDF (which is another W3C standard, with strong relations to OWL) and OWL 1 (the current OWL version is 2); it also supports non standard extensions through a rule reasoner. It could be used to implement an expert system, but it is not, per se, a replacement for Jess or CLIPS.
Side note: Manchester OWL and Protege OWL don't really exist. Protege is a tool for creating OWL ontologies, supporting a number of OWL serialization formats (RDF/XML, OWL/XML, Turtle, Manchester syntax, Functional syntax, and more); Protege OWL is a plugin for an older Protege version - current Protege (5.1) has no 'OWL plugin' - OWL is integrated in the tool itself. Manchester OWL is sometimes used to refer to Manchester syntax for OWL - this is nothing but a name for the format, and does not indicate any difference in expressivity.