Genomics Inform.  2010 Jun;8(2):94-96.

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

• Lee KE
• Jang MH
• Rhie A
• Thong CT
• Yang S
• Park HS

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.

Keyword

systems biology; visualization; common exchange format

MeSH Terms

2,5-Dimethoxy-4-Methylamphetamine
Biology
Computational Biology
Indonesia
Systems Biology
2,5-Dimethoxy-4-Methylamphetamine