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http://dx.doi.org/10.5808/GI.2010.8.2.094

Java DOM Parsers to Convert KGML into SBML and BioPAX Common Exchange Formats  

Lee, Kyung-Eun (Department of Computer Science, Ewha Womans University)
Jang, Myung-Ha (Department of Computer Science, Ewha Womans University)
Rhie, A-Rang (Department of Computer Science, Ewha Womans University)
Thong, Chin Ting (Department of Computer Science, Ewha Womans University)
Yang, San-Duk (Department of Computer Science, Ewha Womans University)
Park, Hyun-Seok (Department of Computer Science, Ewha Womans University)
Publication Information
Genomics & Informatics / v.8, no.2, 2010 , pp. 94-96 More about this Journal
Abstract
Integrating various pathway data collections to create new biological knowledge is a challenge, for which novel computational tools play a key role. For this purpose, we developed the Java-based conversion modules KGML2SBML and KGML2BioPAX to translate KGML (KEGG Markup Language) into a couple of common data exchange formats: SBML (Systems Biology Markup Language) and BioPAX (Biological Pathway Exchange). We hope that our work will be beneficial for other Java developers when they extend their bioinformatics system into SBML- or BioPAX-aware analysis tools. This is part of our ongoing effort to develop an ultimate KEGG-based pathway enrichment analysis system.
Keywords
systems biology; visualization; common exchange format;
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