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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2
Open accessAbstract
Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.
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Self-citation
Metadata
- Authors
- Hucka, M., Bergmann, F. T., Chaouiya, C., Dräger, A., Hoops, S., Keating, S. M., König, M., Novère, N. L., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Sheriff, R., Smith, L. P., Waltemath, D., Wilkinson, D. J., & Zhang, F.
- Affiliations
- California Institute of Technology (US)
- Centre National de la Recherche Scientifique (FR)
- German Center for Infection Research (DE)
- Virginia Tech (US)
- European Bioinformatics Institute (GB)
- Humboldt-Universität zu Berlin (DE)
- Babraham Institute, Cambridge, UK
- University of Utah (US)
- Vrije Universiteit Amsterdam (NL)
- Heidelberg University (DE)
- University of Connecticut (US)
- European Bioinformatics Institute, Cambridge, UK
- University of Washington (US)
- Universitätsmedizin Greifswald (DE)
- Newcastle University (GB)
- National Institutes of Health (US)
- Corresponding author
- Smith, Lucian P.
- ORCID
- Venue
- Journal of Integrative Bioinformatics
- Publisher
- Walter de Gruyter GmbH
- Published
- 2019-06-20
- Volume
- 16
- Issue
- 2
- Pages
- 266-266
- ISSN
- 1432-4385 (ISSN-L)
- 1613-4516
- PMC
- PMC6798823
- OpenAlex
- W2916475656
- Cited by
- 258
- References
- 31
- Citations by year
- 2026: 17 · 2025: 9 · 2024: 25 · 2023: 28 · 2022: 23 · 2021: 38 · 2020: 30 · 2019: 19
- FWCI
- 9.10
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (acceptedVersion, cc-by-nc-nd)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion, cc-by)
- HAL AMU (submittedVersion, cc-by)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- edoc Publication server (Humboldt University of Berlin) (submittedVersion, cc-by)
- VU Research Portal (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- edoc Publication server (Humboldt University of Berlin) (cc-by)
- PUB – Publications at Bielefeld University (Bielefeld University)
- Funders
- Ministry of Education, Culture, Sports, Science and Technology
- Defense Advanced Research Projects Agency
- Biotechnology and Biological Sciences Research Council
- Japan Science and Technology Agency
- National Institute of General Medical Sciences (R01GM077671, R01GM070923, P41GM103313)
- Exploratory Research for Advanced Technology
- Air Force Office of Scientific Research
- Army Research Office
- Institute for Collaborative Biotechnologies
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- SBML, XML data structure, mathematical biology, metabolic pathways, signaling pathways
- MeSH terms
- Animals, Computer Graphics, Documentation, Humans, Models, Biological, Programming Languages, Signal Transduction, Information Storage and Retrieval, Proteome, Internationality, Systems Biology, Biological Ontologies, Datasets as Topic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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