The current knowledge about biochemical networks is largely incomplete. Thus biologists constantly need to revise or extend existing knowledge. The revision and/or extension are first formulated as theoretical hypotheses, then verified experimentally. Recently, biological data have been produced in great volumes and in diverse formats. It is a major challenge for biologists to process these data to reason about hypotheses. Many computer-aided systems have been developed to assist biologists in undertaking this challenge. The majority of the systems help in finding pattern in data and leave the reasoning to biologists. A few systems have tried to automate the reasoning process of hypothesis formation. These systems generate hypotheses from a knowledge base and given observations. A main drawback of these knowledge-based systems is the knowledge representation formalisms they use. These formalisms are mostly monotonic and are now known to be not quite suitable for knowledge representation, especially in dealing with the inherently incomplete knowledge about biochemical networks.