This paper deals with an efficient management and automatic update sub-system for WASPIFA (Web-based Assistant System for Protein-protein Interaction and Function Analysis) system that had been developed in the past and now provides the comprehensive information on protein-protein interaction and protein function. Protein interacting data has increased exponentially, so that it costs enormous time and effort. In other words, it is actually impossible to manually update and manage an analysis system based on protein interacting data. Even though there exists a good analysis system, it could be useless if it was able to be updated timely and managed properly. Unfortunately, in most cases, biologists without professional knowledge on their analysis systems have to cope with a great difficulty in running them. In this respect, the efficient management and automatic update subsystem of protein interacting and its related data has been developed to facilitate experimental biologists as well as bioinformaticians to update and manage the WASPIFA system.