The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

By Michael Hucka, A. Finney, H. Sauro, H. Bolouri, J. Doyle, Hiroaki Kitano, Adam P. Arkin, B. Bornstein, D. Bray, Athel Cornish-Bowden and 33 more. Bioinform., 2003

3,331 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/59dfdb38f27835e4aa4da5da40301c7e0b9a7f0d

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In Molecular Biology

1. Bernhard O. Palsson
2. Huaiyu Mi
3. Paul D. Thomas
4. Anushya Muruganujan
5. V. Schachter
6. Pierre-Yves Bourguignon
7. Maxime Durot
8. Jens Nielsen

Citations in the corpus

• CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks (2008, methodology): “SBML is a tool-neutral computerreadable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell signaling pathways, gene regulatory networks, and other modeling problems in systems biology [2], [3].”
• Reactome knowledgebase of human biological pathways and processes (2008, neutral): “org/Main_Page) (10), Protégé (http://protege.”
• A Correction to the Review Titled "Rules for Modeling Signal-Transduction Systems" by W. S. Hlavacek et al. (2006, background): “Versions of SBML up through Level 2 Version 2, which is presently being finalized, do not provide direct support for compactly representing multiple protein complexes or multiple states of proteins.”
• Universally Sloppy Parameter Sensitivities in Systems Biology Models (2007, methodology): “SBML files and SloppyCell scripts to reproduce all presented calculations are in Dataset S1.”
• BioModels—15 years of sharing computational models in life science (2019, methodology): “BioModels was an early resource to endorse standard formats for encoding models and provided kinetic models encoded in SBML (6).”
• BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models (2010, methodology): “The SBML formats menu (area 2 in Figure 7) allows a user to download the model in various versions of SBML [3].”
• PANTHER Pathway: an ontology-based pathway database coupled with data analysis tools (2009, methodology): “Although SBML and BioPAX provide nice structures for a computer to read pathway information, a pathway diagram is still more appealing to human eyes.”
• A travel guide to Cytoscape plugins (2012, background): “Cytoscape imports interaction data in various generic tabular formats including CSV (comma-separated values), TSV (tab-separated values) and Excel, along with network-specific formats such as SIF (simple interaction file, originally developed for Cytoscape), XGMML (Extensible Graph Markup and Modeli”
• BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems (2005, background): “Example of such formats are CellML (2) and the Systems Biology Markup Language (SBML) (3,4).”
• BiGG Models: A platform for integrating, standardizing and sharing genome-scale models (2015, methodology): “In BiGG, users could export models in the Systems Biology Markup Language (SBML) format (19), visualize metabolic pathways and search the database.”
• Genome-scale models of bacterial metabolism: reconstruction and applications (2008, methodology): “The general-purpose SBML format (Systems Biology Markup Language) (Hucka et al ., 2003) is often used to exchange constraint-based models, thus playing the role of a ‘default’ standard for models.”
• The NCBI BioSystems database (2009, neutral): “Even when databases support well-established data standards such as BioPAX (10) or SBML (11), there are situations where the standards may not provide for encoding of some data, such as pathway graphical images, or allow ambiguity that makes automated import more difficult, such as not explicitly enum”
• Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT (2012, methodology): “The resulting active metabolic networks are provided in SBML [25] format and are available at www.”
• WikiPathways: Pathway Editing for the People (2008, background): “…have the full expressiveness of BioPAX (see the BioPAX Wiki at http://biopaxwiki.org/cgi-bin/ moin.cgi) or Systems Biology Markup Language (SBML) [12], it provides the basic functionality for researchers to create appealing pathway diagrams and to perform basic statistical tests on pathways such…”