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. 2015 Sep;29(9):885-96.
doi: 10.1007/s10822-015-9860-5. Epub 2015 Jul 23.

Activity, assay and target data curation and quality in the ChEMBL database

George Papadatos  1 , Anna Gaulton  1 , Anne Hersey  1 , John P Overington  2
Affiliations

Activity, assay and target data curation and quality in the ChEMBL database

George Papadatos et al. J Comput Aided Mol Des. 2015 Sep.

Abstract

The emergence of a number of publicly available bioactivity databases, such as ChEMBL, PubChem BioAssay and BindingDB, has raised awareness about the topics of data curation, quality and integrity. Here we provide an overview and discussion of the current and future approaches to activity, assay and target data curation of the ChEMBL database. This curation process involves several manual and automated steps and aims to: (1) maximise data accessibility and comparability; (2) improve data integrity and flag outliers, ambiguities and potential errors; and (3) add further curated annotations and mappings thus increasing the usefulness and accuracy of the ChEMBL data for all users and modellers in particular. Issues related to activity, assay and target data curation and integrity along with their potential impact for users of the data are discussed, alongside robust selection and filter strategies in order to avoid or minimise these, depending on the desired application.

Keywords: Data curation; Data quality; Public bioactivity databases.

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Figures

Fig. 1
Fig. 1
The current in-house compound, activity, assay and target curation workflow in ChEMBL production. The steps involved in the activity, assay and target curation branches, along with suggestions on how the users/modellers can utilise these to improve data integrity and minimise or avoid ambiguity are discussed in the following sections
Fig. 2
Fig. 2
The experimental data section of the ChEMBL 20 database schema, showing the columns of the ACTIVITIES and ASSAYS tables
Fig. 3
Fig. 3
A subset of the target information section of the ChEMBL 20 database schema
See this image and copyright information in PMC

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