| Java DOM Parsers to Convert KGML into SBML and BioPAX Common Exchange Formats. |
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Kyung Eun Lee, Myung Ha Jang, Arang Rhie, Chin Ting Thong, Sanduk Yang, Hyun Seok Park |
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Department of Computer Science, Ewha Womans University, Seoul 120-750, Korea. neo@ewha.ac.kr |
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| Abstract |
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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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