An open source chemical structure curation pipeline using RDKit
Authors
Hersey, Anne
Félix, Eloy
Landrum, Greg
Gaulton, Anna
Atkinson, Francis
Bellis, Louisa J.
De Veij, Marleen
Leach, Andrew R.
Publication Date
2020-09-01Journal Title
Journal of Cheminformatics
Publisher
Springer International Publishing
Volume
12
Issue
1
Language
en
Type
Article
This Version
VoR
Metadata
Show full item recordCitation
Bento, A. P., Hersey, A., Félix, E., Landrum, G., Gaulton, A., Atkinson, F., Bellis, L. J., et al. (2020). An open source chemical structure curation pipeline using RDKit. Journal of Cheminformatics, 12 (1)https://doi.org/10.1186/s13321-020-00456-1
Description
Funder: European Molecular Biology Laboratory; doi: http://dx.doi.org/10.13039/100013060
Abstract
Abstract: Background: The ChEMBL database is one of a number of public databases that contain bioactivity data on small molecule compounds curated from diverse sources. Incoming compounds are typically not standardised according to consistent rules. In order to maintain the quality of the final database and to easily compare and integrate data on the same compound from different sources it is necessary for the chemical structures in the database to be appropriately standardised. Results: A chemical curation pipeline has been developed using the open source toolkit RDKit. It comprises three components: a Checker to test the validity of chemical structures and flag any serious errors; a Standardizer which formats compounds according to defined rules and conventions and a GetParent component that removes any salts and solvents from the compound to create its parent. This pipeline has been applied to the latest version of the ChEMBL database as well as uncurated datasets from other sources to test the robustness of the process and to identify common issues in database molecular structures. Conclusion: All the components of the structure pipeline have been made freely available for other researchers to use and adapt for their own use. The code is available in a GitHub repository and it can also be accessed via the ChEMBL Beaker webservices. It has been used successfully to standardise the nearly 2 million compounds in the ChEMBL database and the compound validity checker has been used to identify compounds with the most serious issues so that they can be prioritised for manual curation.
Keywords
Methodology, Chemistry, Curation, ChEMBL, RDKit, Open source, Standardisation
Sponsorship
Wellcome Trust (WT086151/Z/08/Z, WT104104/Z/14/Z)
Identifiers
s13321-020-00456-1, 456
External DOI: https://doi.org/10.1186/s13321-020-00456-1
This record's URL: https://www.repository.cam.ac.uk/handle/1810/309800
Rights
Licence:
https://creativecommons.org/licenses/by/4.0/