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)