A Biological Pathway Data Presentation Based On Four XML Formats

In recent years, the amount of biological data, especially the data of biological networks and pathways, is increasing explosively with the rapid development of technologies of biological science. These data should be stored and shared for analysis, number of file formats for storage are created, in which several XML formats are most valuable, including PSI-MI formats, BioPAX formats, SBML formats and KGML formats, etc. These standard pathway formats, are machine readable and are well used for pathway integration and aggregation as well as visualization, analysis. However, there are miserable for human to read which course problems for biologists to do data screening by hand.PBSK browser is a tool to translate these four formats into human-readable forms for presenting complete file data without any information lost. The browser reads files by AJAX in client; transfers data by reasoner in server, then displays the results via AJAX by HTML table. The browser provides two modes for users, which can be selected due to needs of researchers:statistic mode is used for macro statistics of files and detailed information is shown in detailed mode. The browser uses tree viewer to display data construction of files, and each leaf of the tree contains detailed information of each node. Furthermore, the browser provides functions of section accounting and internal link jump for users to analysis data easily.