We present DISPONTE, a semantics for probabilistic ontolo- gies that is based on the distribution semantics for probabilistic logic programs. In DISPONTE each axiom of a probabilistic ontology is annotated with a probability. The probabilistic theory denes thus a distribution over normal theories (called worlds) obtained by including an axiom in a world with a probability given by the annotation. The probability of a query is computed from this distribution with marginalization. We also present the system BUNDLE for reasoning over probabilistic OWL DL ontologies according to the DISPONTE semantics. BUNDLE is based on Pellet and uses its capability of returning explanations for a query. The explanations are encoded in a Binary Decision Diagram from which the probability of the query is computed.