Brief Reports
Copyright ©2005 Baishideng Publishing Group Inc. All rights reserved.
World J Gastroenterol. Mar 21, 2005; 11(11): 1690-1692
Published online Mar 21, 2005. doi: 10.3748/wjg.v11.i11.1690
HBVPathDB: A database of HBV infection-related molecular interaction network
Yi Zhang, Xiao-Chen Bo, Jing Yang, Sheng-Qi Wang
Yi Zhang, Xiao-Chen Bo, Jing Yang, Sheng-Qi Wang, Beijing Institute of Radiation Medicine, 27 Taiping Street, Haidian District, Beijing 100850, China
Author contributions: All authors contributed equally to the work.
Supported by the grant of the National High Technology R and D Program of China No. 2002AA231051 and the grant of the Science and Technology Program of Zhejiang Province No. 011103001
Correspondence to: Dr. Sheng-Qi Wang, Beijing Institute of Radiation Medicine, 27 Taiping Street, Haidian District, Beijing 100850, China. sqwang@nic.bmi.ac.cn
Telephone: +86-10-66932211 Fax: +86-10-66932211
Received: August 31, 2004
Revised: September 1, 2004
Accepted: November 24, 2004
Published online: March 21, 2005
Abstract

AIM: To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus’ and host’s genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection.

METHODS: The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML).

RESULTS: We present the first version of HBVPathDB, which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1050 molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search, unitized search-are supported by the search engine of the database. The database is freely available at http://www.bio-inf.net/HBVPathDB/HBV/.

CONCLUSION: The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing, visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.

Keywords: Hepatitis B viruses, Pathway database, Molecular interactions