In this paper we present HyperJournal, an Open Source web application for publishing on-line Open Access scholarly journals. In the first part (sections 1, 2 and 3) we briefly describe the project and the software. In sections 4 and 5, we discuss the weaknesses of the current publishing model and the benefits deriving from the adoption of Semantic Web technologies, outlining how the Semantic Web vision can help to overcome the inefficiencies of the current model. In the last two sections (6 and 7), we present two experimental applications, developed on top of HyperJournal, with the purpose of demonstrating how the technologies can affect the daily work of scholars. The first application is a tool for graphically visualizing the network of citations existing between articles and their authors, and for performing bibliometric measurements alternative to the ISI Impact Factor. The second is a tool for automatically extracting references from non-structured textual documents, which is part of a tool-chain for the extraction of hidden semantics.