ChEMBL: towards direct deposition of bioassay data
Open accessAbstract
ChEMBL is a large, open-access bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012, 2014 and 2017 Nucleic Acids Research Database Issues. In the last two years, several important improvements have been made to the database and are described here. These include more robust capture and representation of assay details; a new data deposition system, allowing updating of data sets and deposition of supplementary data; and a completely redesigned web interface, with enhanced search and filtering capabilities.
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The other half of activity endpoints originates from ChEMBLdb and IUPHAR/BPS Guide to Pharmacology.
“The other half originates from ChEMBLdb (27) and the IUPHAR/BPS Guide to Pharmacology (30).”
From DrugCentral 2023 extends human clinical data and integrates veterinary drugs (2023) · cites this paper as [27]
More than 85% (234 drugs) of newly added drugs have external identifiers in PubChem, WHO INN, DrugBank, ChEMBLdb, KEGG, UNII, UMLS, etc.
“More than 85% (234 drugs) of the newly added drugs have external identifiers in PubChem (25), World Health Organization (WHO) International Nonproprietary Names (INN), DrugBank (26), ChEMBLdb (27), KEGG (28), FDA’s Global Substance Registration System—Unique Ingredient Identifier (UNII; https://bit.ly/3MNMqwQ), Unified Medical Language System, UMLS (29), etc. (Table 1).”
From DrugCentral 2023 extends human clinical data and integrates veterinary drugs (2023) · cites this paper as [27]
The CC is limited by the availability of experimental data and the coverage of its source databases.
“In essence, the CC is an alternative representation of the small-molecule knowledge deposited in the public domain and, as such, it is also limited by the availability of experimental data and the coverage of its source databases (e.g., ChEMBL9 or DrugBank10).”
From Bioactivity descriptors for uncharacterized chemical compounds (2021) · cites this paper as [9]
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- Authors
- Mendez, D., Gaulton, A., Bento, A. P., Chambers, J., De Veij, M., Félix, E., Magariños, M. P., Mosquera, J. F., Mutowo, P., Nowotka, M., Gordillo-Marañón, M., Hunter, F., Junco, L., Mugumbate, G., Rodriguez-Lopez, M., Atkinson, F., Bosc, N., Radoux, C. J., Segura-Cabrera, A., Hersey, A., & Leach, A. R.
- Affiliations
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Bioinformatics Institute (GB)
- Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK
- Corresponding author
- Leach, Andrew R
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-11-06
- Volume
- 47
- Issue
- D1
- Pages
- D930-D940
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC6323927
- OpenAlex
- W2900090807
- Cited by
- 2,372
- References
- 28
- Citations by year
- 2026: 306 · 2025: 391 · 2024: 464 · 2023: 439 · 2022: 314 · 2021: 304 · 2020: 125 · 2019: 26 · 2018: 1
- FWCI
- 84.82
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust (WT104104/Z/14/Z)
- National Institutes of Health (U54CA189205)
- European Union Seventh Framework Programme (FP7/2007–2013, 602156)
- Innovative Medicines Initiative Joint Undertaking (115002)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Keywords
- ChEMBL, bioassay data, data deposition
- MeSH terms
- Biological Assay, Periodicals as Topic, User-Computer Interface, Drug Discovery, Databases, Pharmaceutical
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