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. 2020 Jan 8;48(D1):D407-D415.
doi: 10.1093/nar/gkz1055.

BioModels-15 years of sharing computational models in life science

Rahuman S Malik-Sheriff  1 , Mihai Glont  1 , Tung V N Nguyen  1 , Krishna Tiwari  1   2 , Matthew G Roberts  1 , Ashley Xavier  1 , Manh T Vu  1 , Jinghao Men  1 , Matthieu Maire  1 , Sarubini Kananathan  1 , Emma L Fairbanks  1 , Johannes P Meyer  1 , Chinmay Arankalle  1 , Thawfeek M Varusai  1 , Vincent Knight-Schrijver  2 , Lu Li  2 , Corina Dueñas-Roca  1 , Gaurhari Dass  1 , Sarah M Keating  1 , Young M Park  1 , Nicola Buso  1 , Nicolas Rodriguez  1   2 , Michael Hucka  3 , Henning Hermjakob  1   4
Affiliations

BioModels-15 years of sharing computational models in life science

Rahuman S Malik-Sheriff et al. Nucleic Acids Res. .

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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Figures

Figure 1.
Figure 1.
BioModels content and coverage. (A) The cumulative number of models in BioModels over the past 15 years in the curated and non-curated categories. (B) Distribution of models across taxons. (C) GO-based classification of models. (D) Distribution of models across diseases.
Figure 2.
Figure 2.
Model curation and annotation in BioModels. (A) Model curation workflow. (B) Semantic enrichment of models involves cross-referencing model entities (left) with controlled vocabularies and data resources (right) using COMBINE qualifiers (middle) that define the inter-relationship.
Figure 3.
Figure 3.
Provenance of models. BioModels hosts peer-reviewed models from over 300 journals.
Figure 4.
Figure 4.
From submission to publication of a model in BioModels.
See this image and copyright information in PMC

References

    1. Le Novère N. Quantitative and logic modelling of molecular and gene networks. Nat. Rev. Genet. 2015; 16:146–158. - PMC - PubMed
    1. Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B. et al. .. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 2006; 34:D689–D691. - PMC - PubMed
    1. Stanford N.J., Wolstencroft K., Golebiewski M., Kania R., Juty N., Tomlinson C., Owen S., Butcher S., Hermjakob H., Le Novère N. et al. .. The evolution of standards and data management practices in systems biology. Mol. Syst. Biol. 2015; 11:851. - PMC - PubMed
    1. Szigeti B., Roth Y.D., Sekar J.A.P., Goldberg A.P., Pochiraju S.C., Karr J.R.. A blueprint for human whole-cell modeling. Curr. Opin. Syst. Biol. 2018; 7:8–15. - PMC - PubMed
    1. Wilkinson M.D., Dumontier M., Aalbersberg I., Appleton G., Axton M., Baak A., Blomberg N., Boiten J.-W., da Silva Santos L.B., Bourne P.E. et al. .. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data. 2016; 3:160018. - PMC - PubMed

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