Recent developments in the field of Grid computing reveal the strong need of managing metadata on much higher level than it used to be done previously. Standard solutions like MDS provide relatively efficient means of managing Grid resources on a low level basis, usually available for Grid experts and simple search tools. However in order to manage resources among multiple Virtual Organizations composed of highly heterogeneous entities, joining and leaving the Grid in a dynamic manner, a more flexible way of describing and managing their resources is required. In this paper, a solution to this problem based on ontologies and distributed knowledge base is presented. The knowledge base distributed architecture is discussed with the flexibility and fault-tolerance outlined. The performance evaluation for typical use cases shows, that ontology separation and various configurations of GOM make it useful for managing knowledge in multiple domains.