基于XML构建生物信息二级数据库

Building bioinformatics secondary database with XML

提出并实现了一种生物信息二级数据库的构建方法。该方法采用NCBI维护的一级数据库作为核酸和蛋白质序列数据来源，以Oraele9i作为后台软件，所有的应用程序基于Java开发。通过代理程序自动获取Web数据，并以XML作为中间格式保存，然后通过解析提交到二级数据库中，同时转换成便于Web发布的HTML格式。该方法既方便对语义的机器解析，又有效地保证入库信息的完整性，显著提高了二级数据库的开发效率。

This paper presents a method for the construction of bioinformatics secondary database. The method selects the primary databases maintained by America＇s National Center for Biotechnology Information （NCBI） as the main data source, Oracle 9i as the background and Java as the basic programming tool. Web data such as nucleotide and protein sequences are retrieved by agent programs, stored in the extensible markup language （XML） files, then parsed and loaded into the secondary database, and transformed into the hyper text markup language （HTML） files for publishing. Through this method, semantic analysis is simplified and data integrity is guaranteed, thus the efficiency of secondary database construction can be remarkably improved.