Qualitative translation of relations from BioPax to SBML qual

LGPL version 3

Download the converted BioPax files

The Biological Pathway Exchange Language (BioPAX) and the Systems Biology Markup Language (SBML) belong to the most popular modeling and data exchange languages in systems biology. The focus of SBML is quantitative modeling and dynamic simulation of models, whereas the BioPAX specification concentrates mainly on visualization and qualitative analysis of pathway maps. BioPAX describes reactions and relations. In contrast, reactions are the only type of interaction in core SBML. With the SBML Qualitative Models extension (qual), it has recently also become possible to describe relations in SBML. Before the qual creation, relations could not be translated into SBML at all or were erroneously converted to reactions. Until now, there exists no BioPAX to SBML converter that is fully capable of translating both reactions and relations.

Here we present the conversion result of the complete Nature Pathway Interaction Database (PID), which includes pathways from BioCarta, Reactome, and from the National Cancer Institute. All PID BioPax Level 2 and Level 3 pathway files have been translated into the SBML format (Level 3 Version 1) including both reactions and relations by using the new qual extension package.

The webtool BioPAX2SBML for further conversions is available at our Bioinformatics Webservices.

File (Type) Size Release date
  • Translation of BioPax Level 2 NCI files
  • 3.3 MB 2012-10-05
  • Translation of BioPax Level 3 NCI files
  • 3.5 MB 2012-10-05
  • Translation of BioPax Level 2 BioCarta files
  • 2.1 MB 2012-10-05
  • Translation of BioPax Level 3 BioCarta files
  • 2.0 MB 2012-10-05
  • Translation of BioPax Level 2 Reactome files
  • 3.2 MB 2012-10-05
  • Translation of BioPax Level 3 Reactome files
  • 3.5 MB 2012-10-05

    Please cite:

    [1] Finja Büchel, Clemens Wrzodek, Florian Mittag, Andreas Dräger, Johannes Eichner, Nicolas Rodriguez, Nicolas Le Novère, and Andreas Zell. Qualitative translation of relations from BioPAX to SBML qual. Bioinformatics, 28(20):2648--2653, August 2012. [ DOI | details | link | pdf ]

    Data source:

    Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, and Buetow KH: PID: the Pathway Interaction Database. Nucleic Acids Res 2009, 37, D674-D679.