Translation of BioPAX into SBML including the Qualitative Models extension

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 webtool BioPAX2SBML. It is capable of properly translating BioPAX formats (Level 2 and 3) into SBML format (Level 3 Version 1 with qual) including reactions and relations in one model.

We demonstrate the functionality of BioPAX2SBML by converting the whole Nature Pathway Interaction Database (PID), which includes pathways from BioCarta, Reactome, and from the National Cancer Institute, from BioPAX Level 2 and Level 3 formats to the SBML format, including the qual extension. The translated SBML models are freely available at

Please cite: Büchel F, Wrzodek C, Mittag F, Dräger A, Eichner J, Rodriguez N, Le Novère N, and Zell A. Qualitative translation of relations from BioPAX to SBML. Bioinformatics, August 2012. [DOI | details] (buechel - 2012-09-25 17:20)

SBML models: The translated SBML models of the Nature Pathway Interaction Database are freely available at (buechel - 2012-04-02 17:20)

Webservice: The webtool BioPAX2SBML is now available at our Bioinformatics Webservices.   -   (buechel - 2012-04-02 16:02)

Download: Standalone executable jar: Download

This project is promoted by:

BMBF NGFN ZBIT Virtual Liver

LGPL version 3
BioPAX2SBML is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this program. If not, see