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
M. Horridge, T. Tudorache, C. Nyulas, and M. Musen. OWL: Experiences and Directions Workshop (OWLED), volume 1265 of CEUR Workshop Proceedings, page 109-120. CEUR-WS.org, (2014)
P. Monachesi, L. Lemnitzer, and K. Simov. Proceedings of the European Conference on Technology Enhanced Learning (EC-TEL 2006), volume 4227 of Lecture Notes in Computer Science, page 667-672. Springer, (2006)
R. Hoekstra, J. Breuker, M. Bello, and A. Boer. Proceedings of the Workshop on Legal Ontologies and Artificial Intelligence Techniques (LOAIT 2007), (June 2007)
Y. Raimond, S. Abdallah, M. Sandler, and F. Giasson. Proceedings of the 8th International Conference on Music Information Retrieval (ISMIR 2007), page 417--422. Vienna, Austria, (September 2007)