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KMID : 1132720100080020094
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Genomics & Informatics
2010 Volume.8 No. 2 p.94 ~ p.96
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Java DOM Parsers to Convert KGML into SBML and BioPAX Common Exchange Formats
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Lee Kyung-Eun
Jang Myung-Ha
Rhie A-Rang
Thong Chin Ting
Yang San-Duk
Park Hyun-Seok
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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.
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KEYWORD
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systems biology, visualization, common exchange format
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