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Cited by 361Scientific Computing and Data ManagementGene Regulatory Network AnalysisResearch Data Management Practices

BioModels—15 years of sharing computational models in life science

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Malik-Sheriff, Rahuman S, Glont, Mihai, Nguyen, Tung V N, Tiwari, Krishna, Roberts, Matthew G, Xavier, Ashley, Vu, Manh T, Men, Jinghao +16 more·2019·Nucleic Acids Research
DOI 10.1093/nar/gkz1055PMC PMC7145643
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Abstract

Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.ac.uk/biomodels/), a repository for mathematical models, was established in 2005. The current BioModels platform allows submission of models encoded in diverse modelling formats, including SBML, CellML, PharmML, COMBINE archive, MATLAB, Mathematica, R, Python or C++. The models submitted to BioModels are curated to verify the computational representation of the biological process and the reproducibility of the simulation results in the reference publication. The curation also involves encoding models in standard formats and annotation with controlled vocabularies following MIRIAM (minimal information required in the annotation of biochemical models) guidelines. BioModels now accepts large-scale submission of auto-generated computational models. With gradual growth in content over 15 years, BioModels currently hosts about 2000 models from the published literature. With about 800 curated models, BioModels has become the world’s largest repository of curated models and emerged as the third most used data resource after PubMed and Google Scholar among the scientists who use modelling in their research. Thus, BioModels benefits modellers by providing access to reliable and semantically enriched curated models in standard formats that are easy to share, reproduce and reuse.

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  • Model repositories such as BioModels, JWS Online, or PMR2 provide different means to retrieve and use simulation models.

    “Model repositories such as BioModels [10, 11], JWS Online [12], or the Physiome Model Repository 2 (PMR2) [13] provide different means to retrieve and use simulation models.”

    From Relating simulation studies by provenance—Developing a family of Wnt signaling models (2021) · cites this paper as [10]

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Authors
Malik-Sheriff, R. S., Glont, M., Nguyen, T. V. N., Tiwari, K., Roberts, M. G., Xavier, A., Vu, M. T., Men, J., Maire, M., Kananathan, S., Fairbanks, E. L., Meyer, J. P., Arankalle, C., Varusai, T. M., Knight-Schrijver, V., Li, L., Dueñas-Roca, C., Dass, G., Keating, S. M., Park, Y. M., Buso, N., Rodriguez, N., Hucka, M., & Hermjakob, H.
Affiliations
  • European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
  • European Bioinformatics Institute (GB)
  • Babraham Institute (GB)
  • California Institute of Technology (US)
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2019-11-08
Volume
48
Issue
D1
Pages
D407-D415
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkz1055
PMC
PMC7145643
OpenAlex
W2988361147
Cited by
361
References
8
Citations by year
2026: 19 · 2025: 59 · 2024: 71 · 2023: 64 · 2022: 74 · 2021: 50 · 2020: 21 · 2019: 3
FWCI
43.80
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • CaltechAUTHORS (California Institute of Technology) (submittedVersion, cc-by)
Funders
  • Biotechnology and Biological Sciences Research Council (BB/J019305/1, BB/J004456/1, BB/P013384/1, BB/P013406/1, BB/P013414/1, BB/L502224/1)
  • Innovative Medicines Initiative (115156, 116030)
  • European Molecular Biology Laboratory
Topics
  • Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
  • Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
Keywords
biomodels, mathematical model, computational model, model repository, model curation, model reproducibility, SBML, CellML, Miriam, controlled vocabulary, model annotation, model sharing, model reuse
MeSH terms
Biological Science Disciplines, Models, Biological, Programming Languages, Software, User-Computer Interface, Conflict of Interest

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