Title :
PBSK browser: Navigate biological pathways of PSI-MI, BioPAX, SBML and KGML formats
Author :
Huang, Donglin ; Huang, Yiling ; Klukas, Christian ; Hofestädt, Ralf ; Chen, Ming
Author_Institution :
Dept. of Bioinf., Coll. of Life Sci., China
Abstract :
Recently more and more public biological pathway databases support at least one standard pathway format, e.g. PSI-MI, BioPAX and SBML, accessible from either FTP downloads or HTTP downloads. These standard pathway formats are machine readable and are often used for pathway integration and aggregation as well as visualization, analysis, but they are not well-suited for unassisted comprehension and inspection. However it is something miserable for human to read them. It is not easy for us to get knowledge we want from files in these common formats. To address this problem we present a web service named PBSK Browser which is designed to translate BioPAX, SBML, PSI-MI and KGML from machine-readable to human-readable in the form of HTML tables, presenting all detail annotations in the files. PBSK Browser is freely available at http://bis.zju.edu.cn/pbsk.
Keywords :
biochemistry; bioinformatics; database management systems; hypermedia markup languages; molecular biophysics; transport protocols; BioPAX; FTP downloads; HTML tables; HTTP downloads; KGML; PBSK browser; PSI-MI; SBML; biological pathways; human-readable; machine-readable; pathway aggregation; pathway integration; public biological pathway databases support; HTML tables; XML file formats; tree viewer;
Conference_Titel :
Bioinformatics and Biomedicine Workshops (BIBMW), 2010 IEEE International Conference on
Conference_Location :
Hong, Kong
Print_ISBN :
978-1-4244-8303-7
Electronic_ISBN :
978-1-4244-8304-4
DOI :
10.1109/BIBMW.2010.5703766