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Aimming at the difficulty in getting semantic information from each problem in problem set archives, We propose a new method of ontology-based semantic annotation for problem set archives, which utilizes programming knowledge domain ontology to add semantic annotations to problems in the Web. The system we developed adds semantic annotation for each problem in the form of Extensible Makeup Language. Our method overcomes the difficulty of extracting semantics from problem set archives and the efficiency of this method is demonstrated through a case study. Having semantic annotations of problems, a student can efficiently locate the problems that logically correspond to his knowledge.