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BioModels—15 years of sharing computational models in life science

Malik-Sheriff, Rahuman S. and Glont, Mihai and Nguyen, Tung V. N. and Tiwari, Krishna and Roberts, Matthew G. and Xavier, Ashley and Vu, Manh T. and Men, Jinghao and Maire, Matthieu and Kananathan, Sarubini and Fairbanks, Emma L. and Meyer, Johannes P. and Arankalle, Chinmay and Varusai, Thawfeek M. and Knight-Schrijver, Vincent and Li, Lu and Dueñas-Roca, Corina and Dass, Gaurhari and Keating, Sarah M. and Park, Young M. and Buso, Nicola and Rodriguez, Nicolas and Hucka, Michael and Hermjakob, Henning (2020) BioModels—15 years of sharing computational models in life science. Nucleic Acids Research, 48 (D1). D407-D415. ISSN 0305-1048. PMCID PMC7145643. https://resolver.caltech.edu/CaltechAUTHORS:20191111-111825904

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/nar/gkz1055DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145643PubMed CentralArticle
ORCID:
AuthorORCID
Keating, Sarah M.0000-0002-3356-3542
Hucka, Michael0000-0001-9105-5960
Additional Information:© 2019 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received September 22, 2019; Revised October 22, 2019; Editorial Decision October 23, 2019; Accepted November 06, 2019; Published: 08 November 2019. We would like to acknowledge the COMBINE community for the support and numerous contributions over the years. We are also grateful to the libSBML (http://sbml.org/Software/libSBML) and JSBML (http://sbml.org/Software/JSBML) development teams for empowering us to seamlessly develop SBML support in our tools and services. Funding: 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 Joint Undertaking [115156]; European Molecular Biology Laboratory; Innovative Medicines Initiative 2 Joint Undertaking [116030]. Funding for open access charge: Research Councils UK Open Access. Conflict of interest statement. None declared.
Funders:
Funding AgencyGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J019305/1
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J004456/1
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P013384/1
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P013406/1
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P013414/1
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L502224/1
Innovative Medicines Initiative Joint Undertaking115156
European Molecular Biology Laboratory (EMBL)UNSPECIFIED
Innovative Medicines Initiative Joint Undertaking116030
Research Councils UKUNSPECIFIED
Issue or Number:D1
PubMed Central ID:PMC7145643
Record Number:CaltechAUTHORS:20191111-111825904
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20191111-111825904
Official Citation:Rahuman S Malik-Sheriff, Mihai Glont, Tung V N Nguyen, Krishna Tiwari, Matthew G Roberts, Ashley Xavier, Manh T Vu, Jinghao Men, Matthieu Maire, Sarubini Kananathan, Emma L Fairbanks, Johannes P Meyer, Chinmay Arankalle, Thawfeek M Varusai, Vincent Knight-Schrijver, Lu Li, Corina Dueñas-Roca, Gaurhari Dass, Sarah M Keating, Young M Park, Nicola Buso, Nicolas Rodriguez, Michael Hucka, Henning Hermjakob, BioModels—15 years of sharing computational models in life science, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D407–D415, https://doi.org/10.1093/nar/gkz1055
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:99777
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:12 Nov 2019 17:50
Last Modified:15 Apr 2020 16:45

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