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History of science as a formal and autonomous field of research crosses over disciplinary boundaries. For this reason, both its production and its working materials are difficult to classify and catalog according to discipline-based systems of organization of knowledge. Three main problems might be pointed out in this regard: the disciplines themselves are subject to a historical process of transformation; some objects of scientific inquiry resist constraint within rigid disciplinary grids but, rather, extend across several disciplinary boundaries; and the so-called digital revolution has replaced spatial with temporal display sequences and shifted the traditional emphasis on knowledge to user-oriented approaches. The first part of this essay is devoted to a conceptual analysis of the various approaches to the organization of knowledge formulated over time, whereas the second considers the new possibilities afforded by a faceted model of knowledge organization compatible with user-oriented relational databases to the research materials and production of history of science.