@article{Buechel2012a,
  author    = {B\"uchel, Finja and Wrzodek, Clemens and Mittag, Florian and Dr\"ager,
	Andreas and Eichner, Johannes and Rodriguez, Nicolas and {Le Nov\`{e}re},
	Nicolas and Zell, Andreas},
  title     = {{Qualitative translation of relations from BioPAX to SBML qual}},
  journal   = {Bioinformatics},
  publisher = {Oxford University Press},
  year      = {2012},
  volume    = {28},
  pages     = {2648--2653},
  number    = {20},
  month     = aug,
  doi       = {10.1093/bioinformatics/bts508},
  keywords  = {SBML, BioPAX, qual extension, qualitative model, quantitative model,
	conversion},
  pdf       = {https://bioinformatics.oxfordjournals.org/content/28/20/2648.full.pdf},
  url       = {https://bioinformatics.oxfordjournals.org/content/28/20/2648.abstract},
  abstract  = {Motivation: 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, SBML core exclusively describes quantitative
	processes such as reactions. With the SBML Qualitative Models extension
	(qual), it has recently also become possible to describe relations
	in SBML. Before the development of SBML qual, relations could not
	be properly translated into SBML. Until now, there exists no BioPAX
	to SBML converter that is fully capable of translating both reactions
	and relations. Results: The entire Nature Pathway Interaction Database
	(PID) has been converted from BioPAX (Level 2 and Level 3) into SBML
	(Level 3 Version 1) including both reactions and relations by using
	the new qual extension package. Additionally, we present the new
	webtool BioPAX2SBML for further BioPAX to SBML conversions. Compared
	to previous conversion tools, BioPAX2SBML is more comprehensive,
	more robust and more exact. Availability: BioPAX2SBML is freely available
	at \url{http://webservices.cs.uni-tuebingen.de/} and the complete
	collection of the PID models at \url{http://www.cogsys.cs.uni-tuebingen.de/downloads/Qualitative-Models/}.
	Contact: \url{mailto:finja.buechel@uni-tuebingen.de} Supplementary
	Information: Supplementary data is available at Bioinformatics online.},
}