The Semantic Web (SW) deployment is now a realization and the amount of semantic annotations is ever increasing thanks to several initiatives that promote a change in the current Web towards the Web of Data, where the semantics of data become explicit through data representation formats and standards such as RDF/(S) and OWL. However, such initiatives have not yet been accompanied by efficient intelligent applications that can exploit the implicit semantics and thus, provide more insightful analysis. In this paper, we provide the means for efficiently analyzing and exploring large amounts of semantic data by combining the inference power from the annotation semantics with the analysis capabilities provided by OLAP-style aggregations, navigation, and reporting. We formally present how semantic data should be organized in a well-defined conceptual MD schema, so that sophisticated queries can be expressed and evaluated. Our proposal has been evaluated over a real biomedical scenario, which demonstrates the scalability and applicability of the proposed approach.