Jena is a Java framework for building Semantic Web applications. It provides a programmatic environment for RDF, RDFS and OWL, SPARQL and includes a rule-based inference engine.
The OWL API is a Java API and reference implmentation for creating, manipulating and serialising OWL Ontologies. The latest version of the API is focused towards OWL 2
F. Bry, F. Fages, M. Marchiori, and H. Ohlbach. Principles and Practices of Semantic Web Reasoning, volume 05371 of Dagstuhl Seminar Proceedings, Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany, (2005)
R. Pan, Z. Ding, Y. Yu, and Y. Peng. Proceedings of the 4th International Semantic Web Conference (ISWC-2004), volume 3729 of LNCS, page 563--577. Berline (Germany), Springer-Verlag, (2004)
R. Pan, Z. Ding, Y. Yu, and Y. Peng. International Semantic Web Conference, volume 3729 of Lecture Notes in Computer Science, page 563-577. Springer, (2005)
J. Kietz, A. Maedche, and R. Volz. Proc. of Workshop Ontologies and Text, co-located with the 12th International Workshop on Knowledge Engineering and Knowledge Management (EKAW'2000), Juan-Les-Pins, France, (October 2000)
B. Omelayenko, and D. Fensel. Proceedings of the Second Internacional Conference on Electronic Commerce and Web Technologies (ECWEB-2001), Munich (Germany), Springer-Verlag, (2001)