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Genomics Inform > Volume 8(2); 2010 > Article
DOI: https://doi.org/10.5808/gi.2010.8.2.094   
Java DOM Parsers to Convert KGML into SBML and BioPAX Common Exchange Formats.
Kyung Eun Lee, Myung Ha Jang, Arang Rhie, Chin Ting Thong, Sanduk Yang, Hyun Seok Park
Department of Computer Science, Ewha Womans University, Seoul 120-750, Korea. neo@ewha.ac.kr
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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