Building a compendium of expert driven read-across cases to facilitate an analysis of the contribution that different similarity contexts play in read-across performance

Read-across is a data-gap filling technique used to predict the toxicity of a target chemical based on data from similar analogues. It is predominantly performed through expert-driven assessments which can limit reproducibility and broader acceptance. Data-driven approaches such as Generalised Read-Across (GenRA) offer the potential to generate more reproducible read-across predictions with quantified uncertainties and performance metrics. A key challenge is reconciling expert- and data-driven approaches particularly in how analogues are identified, evaluated and used to derive predictions. A critical aspect of analogue selection lies in understanding the relative contribution of different similarity contexts e.g. whether structural similarity plays a larger role than metabolism similarity. This study explored these considerations by compiling a compendium of expert-driven read-across assessments for repeated dose toxicity endpoints from peer reviewed and grey literature. Pairwise similarity was quantified across structural, physicochemical, metabolic and reactivity features within each case and a prediction model was developed to evaluate the contribution of each similarity context in analogue selection. Although the dataset comprised 157 read-across cases and 695 unique substances, it was limited in size, heterogeneous in origin and variable in analogue selection criteria and use contexts. These factors constrain generalisability of the findings and indicate that conclusions should be interpreted with caution. Nonetheless, the qualitative insight that structure and metabolism were influential led to a followup investigation using graph-based deep learning to explore whether embeddings derived from structure and/or metabolism information could improve read-across predictions, using repeated dose toxicity as a case study, relative to structural similarity baselines.