Software Agents for Bioinformatics

Abstract

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 create valuable biological knowledge is one of the most critical issues in bioinformatics. Recently 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 on the World Wide Web. Wrapper construction 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. This talk provides a solution for rapidly building Web wrappers for biological information integration systems and other applications. We defined an XML-based language called WNDL providing a representation of a set of Web pages and data on these pages, as well as how to locate the data, extract the data and combine the data. By executing different scripts, users can automate almost all types of Web browsing behaviors. Since the executor kernal can handle dynamically generated HTTP request parameters, cookies, and illy-structured HTML, our wrapper agents can access commercial biological Web sites as well. We built a variety of biological applications to demonstrate the feasibility of our approach. The software is available at http://chunnan.iis.sinica.edu.tw/software.html or by contacting the speaker.