Biomodels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
Open accessAbstract
BioModels Database (http://www.ebi.ac.uk/biomodels/), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and gives the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML format, and import/export facilities are being developed to extend the spectrum of formats supported by the resource.
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There are notable examples where collaborations have been very successful, such as SBML, BioModels Database or the DREAM challenges.
“There are several notable examples where collaborations have been very successful, such as SBML [238], BioModels Database [239] or the DREAM challenges [94].”
From Reverse engineering and identification in systems biology: strategies, perspectives and challenges (2014) · cites this paper as [239]
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Cites
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Minimum information requested in the annotation of biochemical models (MIRIAM)
Novère, N. L., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P., et al. (2005) · Nature Biotechnology · doi:10.1038/nbt1156 · Cited by 622 · see citing works
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Web-based kinetic modelling using JWS Online
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Systems biology markup language: Level 2 and beyond
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Schema representing the cascading search strategy
Le Novère, N., Bornstein, B., Broicher, A., et al. (2011) · Figshare · doi:10.6084/m9.figshare.6858.v1 · Cited by 1 · see citing works
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Universally Sloppy Parameter Sensitivities in Systems Biology Models
Gutenkunst, R. N., Waterfall, J. J., Casey, F. P., Brown, K. S., Myers, C. R., & Sethna, J. P. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030189 · Cited by 1,261 · see citing works
“Models discussed that are in the BioModels database [42] are: (a) BIOMD0000000005, (c) BIOMD0000000003, (d) BIOMD0000000035, (e) BIOMD0000000002, (f) BIOMD0000000010, (h) BIOMD0000000021, (i) BIOMD0000000033, (k) BIOMD0000000022, (l) BIOMD0000000055, (n) BIOMD0000000015, (o) BIOMD0000000051, (p) BIOMD0000000056, (q) B…”
BackgroundMethodFeedback between p21 and reactive oxygen production is necessary for cell senescence
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“The model is available in the public space of the BASIS database (urn:basis.ncl:basis:6178) and is also obtainable from Biomodels (MODEL 5989624192), http://www.ebi.ac.uk/biomodels/ (Le Novere et al, 2006).”
The BioPAX community standard for pathway data sharing
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Minimum information requested in the annotation of biochemical models (MIRIAM)
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Rules for Modeling Signal-Transduction Systems
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“As an example, the number of models deposited in BioModels Database (Le Novère et al, 2006; Li et al, 2010a) is doubling roughly every 22 months while the average number of relationships between variables per model is doubling every 13 months.”
MethodSelf-citationBioModels: ten-year anniversary
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Towards reproducible computational drug discovery
Schaduangrat, N., Lampa, S., Simeon, S., Gleeson, M. P., Spjuth, O., & Nantasenamat, C. (2020) · Journal of Cheminformatics · doi:10.1186/s13321-020-0408-x · Cited by 208 · see citing works
PTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K
Malek, M., Kielkowska, A., Chessa, T., Anderson, K. E., Barneda, D., Pir, P., Nakanishi, H., Eguchi, S., Koizumi, A., Sasaki, J., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.09.024 · Cited by 190 · see citing works
Sloppy models, parameter uncertainty, and the role of experimental design
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cPath: open source software for collecting, storing, and querying biological pathways
Cerami, E. G., Bader, G. D., Gross, B. E., & Sander, C. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-497 · Cited by 125 · see citing works
Erdemir, A., Mulugeta, L., Ku, J. P., Drach, A., Horner, M., Morrison, T. M., Peng, G. C. Y., Vadigepalli, R., Lytton, W. W., & Myers, J. G. (2020) · Journal of Translational Medicine · doi:10.1186/s12967-020-02540-4 · Cited by 118 · see citing works
Molecular machines or pleiomorphic ensembles: signaling complexes revisited
Mayer, B. J., Blinov, M. L., & Loew, L. M. (2009) · Journal of Biology · doi:10.1186/jbiol185 · Cited by 85 · see citing works
GSK3 and p53 - is there a link in Alzheimer's disease?
Proctor, C. J., & Gray, D. A. (2010) · Molecular Neurodegeneration · doi:10.1186/1750-1326-5-7 · Cited by 80 · see citing works
Kell, D. B. (2007) · IUBMB Life · doi:10.1080/15216540701694252 · Cited by 52 · see citing works
A reappraisal of how to build modular, reusable models of biological systems.
Neal, M. L., Cooling, M. T., Smith, L. P., Thompson, C. T., Sauro, H. M., Carlson, B. E., Cook, D. L., & Gennari, J. H. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003849 · Cited by 49 · see citing works
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)
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Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media
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Adapting modeling and simulation credibility standards to computational systems biology
Tatka, L. T., Smith, L. P., Hellerstein, J. L., & Sauro, H. M. (2023) · Journal of Translational Medicine · doi:10.1186/s12967-023-04290-5 · Cited by 25 · see citing works
Reproducible Research Using Biomodels
Mendes, P. (2018) · Bulletin of Mathematical Biology · doi:10.1007/s11538-018-0498-z · Cited by 20 · see citing works
Recent advances in biomedical simulations: a manifesto for model engineering
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SBML and CellML translation in Antimony and JSim
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- Authors
- Le Novere, N.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-01-01
- Volume
- 34
- Issue
- 90001
- Pages
- D689-D691
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC1347454
- OpenAlex
- W2107062718
- Cited by
- 762
- References
- 10
- Citations by year
- 2026: 10 · 2025: 10 · 2024: 17 · 2023: 19 · 2022: 17 · 2021: 26 · 2020: 28 · 2019: 26 · 2018: 28 · 2017: 33 · 2016: 35 · 2015: 43 · 2014: 37 · 2013: 60 · 2012: 50
- FWCI
- 15.94
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- University of Hertfordshire Research Archive (University of Hertfordshire) (submittedVersion, public-domain)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- BioModels Database, biochemical systems, cellular systems, model curation, SBML, controlled vocabulary, model annotation, model exchange format
- MeSH terms
- Biochemical Phenomena, Cell Physiological Phenomena, Genes, Kinetics, Models, Biological, User-Computer Interface, Databases, Factual, Vocabulary, Controlled, Internet
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