A variant annotation strategy parallel to that of ChEMBL was developed that extracted 82.65% of the original variant annotations from the assay descriptions, which reinforced the confidence in the original ChEMBL variant annotation pipeline (which delivers these annotations by manual extraction of protein variant information from original papers). A clear advantage in the ChEMBL pipeline was the access to expert knowledge to rescue variants otherwise missed by a regular expression match. For example, sequence number shifts and non-canonical amino acid substitution definitions were identified among these expert rescues. However, misannotations reported by ChEMBL were also identified, for example, derived from mistakenly linking assays to protein families rather than single proteins. The current annotation strategy also retrieved several substitutions that had not been previously reported in ChEMBL 31. Nevertheless, these results need to be considered cautiously since they are based on fields previously extracted by ChEMBL rather than the original source in the literature and might miss important aspects of the experimental set-up. Importantly, this approach also relies on accurate reporting of tested variants in the scientific literature in order for their subsequent capture in bioactivity databases. Collaborative work such as reported here is key to improving the ChEMBL database for the wider community; for future releases of ChEMBL we will aim to improve and enhance our reporting of variant data based upon the findings in this paper .