DocumentCode
2377640
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
fYear
2010
fDate
18-18 Dec. 2010
Firstpage
13
Lastpage
18
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;
fLanguage
English
Publisher
ieee
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
Type
conf
DOI
10.1109/BIBMW.2010.5703766
Filename
5703766
Link To Document