The ChEMBL database is a freely available bioactivity database containing close to 2.5 million compound records on nearly 2 million unique chemical structures. 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. The code is available in a GitHub repository and it can also be accessed via the ChEMBL Beaker webservices. ConclusionĪll the components of the structure pipeline have been made freely available for other researchers to use and adapt for their own use. 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. 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. ResultsĪ chemical curation pipeline has been developed using the open source toolkit RDKit. 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.
Incoming compounds are typically not standardised according to consistent rules. The ChEMBL database is one of a number of public databases that contain bioactivity data on small molecule compounds curated from diverse sources.
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