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This paper describes GoNTogle, a framework for document annotation and retrieval, built on top of Semantic Web and IR technologies. GoNTogle supports ontology-based annotation for documents of several formats, in a fully collaborative environment. It provides both manual and automatic annotation mechanisms. Automatic annotation is based on a learning method that exploits user annotation history and textual information to automatically suggest annotations for new documents. GoNTogle also provides search facilities beyond the traditional keyword-based search. A flexible combination of keyword-based and semantic-based search over documents is proposed in conjunction with advanced ontology-based search operations. The proposed methods are implemented in a fully functional tool and their effectiveness is experimentally validated.