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This paper studies the knowledge representation with ontology method in the Protégé 2000 system. We first analyzed the various ontological methods for knowledge representation. Then we described the OWL method used in Protégé 2000 for knowledge representation. We proposed the new method named problem-solving evolutionary method (PSEM) for knowledge representation in which it is based the OWL of Protégé 2000. Then we design the interface between the Racer inference engine and the Protégé 2000. Based on the interface built, we can use the Racer inferring engine to reasoning the knowledge. We use the PSEM to experiment the professional domain knowledge of MIS in which it is based undergraduate level. Experiments have shown that PSEM based on the Protégé 2000 is able to represent some domain knowledge well and built knowledge with OWL can be inferred by the Racer.