Despite its benefits, ToxCast is not without limitations. The program relies heavily on in vitro data, which may not fully replicate the complex interactions occurring in living organisms. As a result, predictions about in vivo toxicity might not always be accurate. Additionally, ToxCast's focus on specific biological pathways means it might overlook chemicals that exert toxicity through less understood or untested mechanisms. There is also the challenge of interpreting the vast amount of data generated, which requires sophisticated computational models and expert analysis.
