A variety of biological data is transferred and exchanged in overwhelming volumes on the World Wide Web. How to rapidly capture, utilize, and integrate the information on the Internet to discover valuable biological knowledge is one of the most critical issues in bioinformatics. Many information integration systems have been proposed for integrating biological data. These systems usually rely on an intermediate software layer called wrappers to access connected information sources. Wrapper construction for Web data sources is often specially hand coded to accommodate the differences between each Web site. However, programming a Web wrapper requires substantial programming skill, and is time-consuming and hard to maintain. In this article we provide a solution for rapidly building software agents that can serve as Web wrappers for biological information integration. We define an XML-based language called Web Navigation Description Language (WNDL), to model a Web-browsing session. A WNDL script describes how to locate the data, extract the data, and combine the data. By executing different WNDL scripts, we can automate virtually all types of Web-browsing sessions. We also describe IEPAD (Information Extraction Based on Pattern Discovery), a data extractor based on pattern discovery techniques. IEPAD allows our software agents to automatically discover the extraction rules to extract the contents of a structurally formatted Web page. With a programming-by-example authoring tool, a user can generate a complete Web wrapper agent by browsing the target Web sites. We built a variety of biological applications to demonstrate the feasibility of our approach.