In this paper we describe the main aspects of a system to perform non-trivial segmentations of 3D surface meshes and to annotate the detected parts through concepts expressed by an ontology. Each part is connected to an instance in a knowledge base to ease the retrieval process in a semantics-based context. Through an intuitive interface, users create such instances by simply selecting proper classes in the ontology; attributes and relations with other instances can be computed automatically based on a customizable analysis of the underlying topology and geometry of the parts.