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
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.
TunedIT is a data & algorithm repository, with benchmark results, experiments and online competitions. Datasets in arff, csv, weka formats. Neural networks, svm, decision trees and other algorithms
G. Pirrò, and J. Euzenat. Proceedings of the 9th International Semantic Web Conference (ISWC2010), volume 6496 of Lecture Notes in Computer Science, page 615-630. Springer, (2010)