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The current manual for Protégé 4 is:
- Matthew Horridge et al. 2009. A Practical Guide To Building OWL Ontologies Using Protégé 4 and CO-ODE Tools, Edition 1.2, published by the University of Manchester, 13 Mar 2009, 109 pp.
- You may also want to inspect the general entry page for these Protégé materials.