BioModels: ten-year anniversary
Open accessAbstract
BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models of biological processes. A large set of models is curated to verify both correspondence to the biological process that the model seeks to represent, and reproducibility of the simulation results as described in the corresponding peer-reviewed publication. Many models submitted to the database are annotated, cross-referencing its components to external resources such as database records, and terms from controlled vocabularies and ontologies. BioModels comprises two main branches: one is composed of models derived from literature, while the second is generated through automated processes. BioModels currently hosts over 1200 models derived directly from the literature, as well as in excess of 140,000 models automatically generated from pathway resources. This represents an approximate 60-fold growth for literature-based model numbers alone, since BioModels' first release a decade ago. This article describes updates to the resource over this period, which include changes to the user interface, the annotation profiles of models in the curation pipeline, major infrastructure changes, ability to perform online simulations and the availability of model content in Linked Data form. We also outline planned improvements to cope with a diverse array of new challenges.
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- Authors
- Chelliah, V., Juty, N., Ajmera, I., Ali, R., Dumousseau, M., Glont, M., Hucka, M., Jalowicki, G., Keating, S., Knight-Schrijver, V., Lloret-Villas, A., Natarajan, K. N., Pettit, J.-B., Rodriguez, N., Schubert, M., Wimalaratne, S. M., Zhao, Y., Hermjakob, H., Le Novère, N., & Laibe, C.
- Affiliations
- European Bioinformatics Institute (GB)
- California Institute of Technology (US)
- Babraham Institute (GB)
- Corresponding author
- Chelliah, Vijayalakshmi
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-11-20
- Volume
- 43
- Issue
- D1
- Pages
- D542-D548
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC4383975
- OpenAlex
- W2147814423
- Cited by
- 281
- References
- 28
- Citations by year
- 2025: 10 · 2024: 5 · 2023: 13 · 2022: 13 · 2021: 22 · 2020: 41 · 2019: 46 · 2018: 37 · 2017: 40 · 2016: 41 · 2015: 13
- FWCI
- 12.99
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion, cc-by)
- Funders
- California Institute of Technology
- University of Connecticut
- European Molecular Biology Laboratory
- European Commission (312455, 305299, 115156)
- Universiteit Stellenbosch
- Innovative Medicines Initiative (115156)
- Directorate for Biological Sciences
- Biotechnology and Biological Sciences Research Council (BB/F010516/1, BB/K016946/1, BB/J019305/1, 1443802)
- National Institute of General Medical Sciences (R01GM070923)
- 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 › Biomedical Text Mining and Ontologies
- Keywords
- biomodels, model repository, model curation, model annotation, web-based simulation, linked data
- MeSH terms
- Computer Simulation, Models, Biological, Databases, Factual, Internet
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