User-Centered Biological Information Location by Combining User Profiles and Domain Knowledge

To aid researchers in obtaining, organizing and managing biological data, we have designed an intelligent digital library system that utilizes advanced data mining techniques. Our digital library system is implemented as a centralized J2EE web application with links to publicly accessible data repositories on the Internet. The digital library is based on a framework used for conventional libraries and an object-oriented paradigm, and provides personalized user-centered services based on the user’s areas of interests and preferences. To make personalized service possible, a “user profile” that represents the preferences of an individual user is constructed based upon a user’s past activities, goals indicated by the user, and options. Utilizing these user profiles, our system makes relevant information available to the user in an appropriate form, amount, and level of detail with minimal user effort. The core of our project is an agent architecture that provides advanced services by combining data mining capabilities with domain knowledge in the form of a semantic network. The semantic network imparts a knowledge structure through which the system can “reason” and draw conclusions about biological data objects and provides a federated view of the many disparate databases of interest to biologists. In the development of our semantic network, we have included the concepts from several established controlled vocabularies, chief among them being the National Library of Medicine’s Unified Medical language System (UMLS). Our complete semantic network consists of 183 semantic types and 69 re-