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ONCOCIN is a rule-based expert system to advise on cancer chemotherapy. Although shown to provide excellent advice, the program could not be easily adapted to critique a physician's treatment plan without incorporation of additional knowledge of the structure of experimental protocols. A separate effort to automate the encoding of new oncology protocols was impeded by the lack of structural organization in the knowledge base. In both cases, problems arose because ONCOCIN's knowledge representation scheme did not reflect the hierarchy of control knowledge inherent in oncology protocols. The limitations of current knowledge representation techniques in ONCOCIN are discussed. In ONCOCIN is a medical expert system that assists physicians In the treatment of cancer patients enrolled in chemotherapy protocols.