updateBASE : Real-time automatic updating system of biological databases under the client-server environment.
Sujin Chae1, Mira Roh2, Ji-Hoon Jun, Geunwoo Lee, Yong-ho In
1sujin@bioinfomatix.com, Bioinfomatix Inc.; 2mrroh@bioinfomatix.com, Bioinfomatix Inc.
The exponential growth of public biological databases leads to problems of frequent local updates. It has been known that most updated database releases often contain newly annotated entries. The prediction of gene functions using local annotation system have been limited due to the gap between public and local database contents. To overcome such limitation, we developed the updateBASE system which provides real-time, automatic updating of biological databases. This system is a client-server architecture. User indicates database name, URL, updating interval, id, password and requests the updating. Server monitors the original database site over network and checks the release date and compares to the date of local database and executes downloading process. After transfer the updated versions of flat files to the local server, reformatting and parsing of the files are processed depending on the purpose of files - searching blast, searching protein domain or making relational database. The system can be implemented to any local annotation system as an independent module. We tested the system to the high-throughput EST analysis system, microbial genome annotation system and integrated metabolic database system. The status of database updating in each annotation system can be traced automatically in real-time. An annotator can get up-to-date database sources and get more confident annotation results using this system. The updateBASE will do effective supporting role in predicting functions and relationships of unknown sequences. The updateBASE is developed by JAVA language on the IBM Netfinity operating LINUX system. Updating history is managed in the MySQL DBMS and socket protocol is used for data monitoring and FTP for file transfer.