Qualitative translation of relations from BioPax to SBML qual |
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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 |
---|---|---|
3.3 MB | 2012-10-05 | |
3.5 MB | 2012-10-05 | |
2.1 MB | 2012-10-05 | |
2.0 MB | 2012-10-05 | |
3.2 MB | 2012-10-05 | |
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.