• 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