Qualitative translation of relations from BioPAX to SBML qual
Open accessAbstract
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 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 with previous conversion tools, BioPAX2SBML is more comprehensive, more robust and more exact. Availability: BioPAX2SBML is freely available at http://webservices.cs.uni-tuebingen.de/ and the complete collection of the PID models is available at http://www.cogsys.cs.uni-tuebingen.de/downloads/Qualitative-Models/. Contact: finja.buechel@uni-tuebingen.de Supplementary Information: Supplementary data are available at Bioinformatics online.
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Whereas SBML and CellML focus on quantitative modelling and dynamic simulation, BioPAX concentrates primarily on quantitative processes and visualization.
“Whereas SBML and CellML focus on quantitative modelling and dynamic simulation, BioPAX concentrates primarily on quantitative processes and visualization [15, 30].”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [30]
The Abstract says BioPAX focuses on visualization and qualitative analysis, not quantitative processes; it assigns quantitative processes to SBML core. The Introduction likewise describes BioPAX as mainly used for qualitative analysis and information exchange. These passages do not address CellML. (LLM, conf=0.90)
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- Authors
- Büchel, F., Wrzodek, C., Mittag, F., Dräger, A., Eichner, J., Rodriguez, N., Le Novère, N., & Zell, A.
- Affiliations
- European Bioinformatics Institute (GB)
- 1 Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 Tübingen, Germany and 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Corresponding author
- Büchel, Finja
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-08-24
- Volume
- 28
- Issue
- 20
- Pages
- 2648-2653
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC3467751
- OpenAlex
- W2157904870
- Cited by
- 22
- References
- 18
- Citations by year
- 2024: 2 · 2023: 1 · 2022: 1 · 2020: 1 · 2018: 1 · 2017: 2 · 2016: 2 · 2015: 2 · 2014: 5 · 2013: 4 · 2012: 1
- FWCI
- 1.54
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/J019305/1, BB/F023545/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- BioPAX, qualitative modeling, SBML, pathway maps, model transformation, web-based tool
- MeSH terms
- Humans, Programming Languages, Software, Databases, Factual, Internet, Systems Biology
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