An open source chemical structure curation pipeline using RDKit
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Journal of Cheminformatics Open Access
METHODOLOGY
An open source chemical structure curation pipeline using RDKit A. Patrícia Bento1 , Anne Hersey1, Eloy Félix1, Greg Landrum2, Anna Gaulton1, Francis Atkinson1,3, Louisa J. Bellis1,4, Marleen De Veij1 and Andrew R. Leach1*
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: Chemistry, Curation, ChEMBL, RDKit, Open source, Standardisation Introduction The ChEMBL database is a freely available bioactivity database containing close to 2.5 million compound records on nearly 2 million unique chemical structures [1]. The compound structures and associated bioactivity data are extracted on a regular basis primarily from the medicinal chemistry literature. A growing number of researchers are also depositing experimental data directly in order to make these available in the public domain. *Correspondence: [email protected] 1 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridgeshire, UK Full list of author information is available at the end of the article
Furthermore, ChEMBL contains a set of manually curated marketed drugs and clinical candidates as well as selected bioactivity data from other public databases such as BindingDB [2] and PubChem [3]. Bioactivity data on the same compound from all ChEMBL sources (scientific articles, deposited datasets and curated drug sources) are aggregated according to chemical structure. Compounds may be physically tested in bi
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