Java DOM Parsers to Convert KGML into SBML and BioPAX Common Exchange Formats.
- Author:
Kyung Eun LEE
1
;
Myung Ha JANG
;
Arang RHIE
;
Chin Ting THONG
;
Sanduk YANG
;
Hyun Seok PARK
Author Information
1. Department of Computer Science, Ewha Womans University, Seoul 120-750, Korea. neo@ewha.ac.kr
- Publication Type:Note
- Keywords:
systems biology;
visualization;
common exchange format
- MeSH:
2,5-Dimethoxy-4-Methylamphetamine;
Biology;
Computational Biology;
Indonesia;
Systems Biology
- From:Genomics & Informatics
2010;8(2):94-96
- CountryRepublic of Korea
- Language:English
-
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.
