Ames Mutagenicity Dataset with Strain-Specific Labels

Description

This dataset contains Ames mutagenicity data for 7858 compounds. It contains their SMILES string, data source, strain-specific Ames test results for Salmonella Typhimurium strains TA98, TA100, TA102, TA1535, and TA1537, and the overall (consensus) Ames test result. We utilized this data to develop a machine learning model for predicting Ames test results, and the data partitions (train, internal (validation) and external (test)) we utilized are also included. This data can be used by researchers developing models to predict the results of the Ames test, specifically considering the outcomes of individual strains. Dataset sources include ISSSTY (ISSTOX Chemical Toxicity Databases, Istituto Superiore di Sanitá https://www.iss.it/isstox), Hansen (Hansen, K., Mika, S., Schroeter, T., Sutter, A., ter Laak, A., Steger-Hartmann, T., Heinrich, N., Muller, K.-R. Benchmark data set for in silico prediction of Ames mutagenicity. Journal of Chemical Information and Modeling 2009,49, 2077–2081, DOI: 10.1021/ci900161g), and EURL (Madia, F., Kirkland, D., Morita, T., White, P., Asturiol, D., Corvi, R. EURL ECVAM Genotoxicity and Carcinogenicity Database of Substances Eliciting Negative Results in the Ames Test: Construction of the Database. Mutation Research: Genetic Toxicology and Environmental Mutagenesis 2020, 854-855, 503199, DOI: 10.1016/j.mrgentox.2020.503199). This is an augmented version of the original dataset developed by Martínez et al. (Martínez, M. J., Sabando, M. V., Soto, A. J., Roca, C., Requena-Triguero, C., Campillo, N. E., Páez, J. A., Ponzoni, I. Multitask deep neural networks for Ames mutagenicity prediction. Journal of Chemical Information and Modeling 2022, 62, 6342–6351, DOI: 10.1021/acs.jcim.2c00532.) The original dataset is available here: https://data.mendeley.com/datasets/ktc6gbfsbh/2 The original Martínez dataset contains strain-specific data for 5536 compounds, which originated from the ISSSTY dataset, and were preprocessed and cleaned as described in the publication. We retained those compounds here, and added additional Ames-negative examples from the Hansen and EURL datasets. We assume here that if the overall Ames result is negative, the strain-specific results are negative as well. We specifically obtained this augmented data from the dataset published by Thompson et al. (Thompson, L. A., Evans, J. G., Matthews, S. T. AmesFormer: State-of-the-art mutagenicity prediction with graph transformers. Chemical Research in Toxicology 2025, 38, 1167–1182, DOI: 10.1021/acs.chemrestox.4c00466). The data labels are 0, 1, and -1. 0 corresponds to non-mutagenic, 1 corresponds to mutagenic, and -1 is undefined. The -1 label was defined based on Martínez et al. and encompasses inconclusive and equivocal experimental results.

Institutions

• Consejo Superior de Investigaciones Científicas

  Madrid, Madrid
• Instituto de Ciencia de Materiales de Madrid

  Madrid, Madrid
• Centro de Investigaciones Biológicas Margarita Salas

  Madrid, Madrid

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