KEGG API: A Web Service Using SOAP/WSDL to Access the KEGG System

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We have been making the KEGG system available at GenomeNet [2]. KEGG is a suite of databases including GENES, SSDB, PATHWAY, LIGAND, LinkDB, etc. for genome research and related research areas in molecular and cellular biology. These databases and associated computation services are available via WWW and the user interfaces are built on web browsers. Thus, the interfaces are designed to be accessed by humans, not by machines, which means that it is troublesome for the researchers who want to use KEGG in an automated manner. Besides, from the database developer’s side, it is impossible to prepare all the CGI programs that satisfy a variety of users’ needs. In recent years, the Internet technology for application-to-application communication referred to as the web service is improving at a rapid rate. For example, Google, a popular Internet search engine, provides the web service called the Google Web API [1]. The service enables users to develop software that accesses and manipulates a massive amount of web documents that are constantly refreshed. In the field of genome research, the web service has attracted an increasing attention [3]. For example, the web service called DAS (distributed annotation system) has been used on several web sites, including Ensembl, Wormbase, Flybase, SGD and TIGR. With the background and the trends noted above, we have started developing a new web service called KEGG API [5]. Using KEGG API, the user can access to all the resources stored in KEGG as a batch processing style without any limitations that the interactive CGI programs will suffer. This also means that the user can embed the KEGG system into in-house programs to analyze his/her own data with KEGG. The program using KEGG API always accesses the up-to-date databases on the KEGG server, no database update or synchronization is required on the client side to use the latest database.