enviPath is a widely used database and prediction system for microbial biotransformation pathways of primarily xenobiotic compounds. Data and prediction system are freely available both via a web interface and a public REST API. Since its initial release in 2016, we extended the data available in enviPath and improved the performance of the prediction system and usability of the overall system. We now provide three diverse data sets, covering microbial biotransformation in different environments and under different experimental conditions. This also enabled developing a pathway prediction model that is applicable to a more diverse set of chemicals. In the prediction engine, we implemented a new evaluation tailored towards pathway prediction, which returns a more honest and holistic view on the performance. We also implemented a novel applicability domain algorithm, which allows the user to estimate how well the model will perform on their data. Finally, we improved the implementation to speed up the overall system and provide new functionality via a plugin system. The main scientific contributions are the development of a pathway prediction model applicable to diverse chemicals, a specialized evaluation method for holistic performance assessment, and a novel applicability domain algorithm for user-specific performance estimation. The introduction of two new data sets, and the creation of links to EC classes make enviPath a unique resource in microbial biotransformation research.

中文翻译：

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生物转化途径预测的进展：enviPath 中的增强功能、数据集和新颖功能


enviPath 是一种广泛使用的数据库和预测系统，用于主要外源化合物的微生物生物转化途径。数据和预测系统可通过 Web 界面和公共 REST API 免费获取。自 2016 年首次发布以来，我们扩展了 enviPath 中的可用数据，并提高了预测系统的性能和整个系统的可用性。我们现在提供三个不同的数据集，涵盖不同环境和不同实验条件下的微生物生物转化。这也使得开发适用于更多样化的化学品的途径预测模型成为可能。在预测引擎中，我们实施了针对路径预测的新评估，它返回了关于性能的更诚实和全面的视图。我们还实现了一种新颖的适用性域算法，该算法允许用户估计模型对其数据的执行情况。最后，我们改进了实现，以加快整个系统的速度，并通过插件系统提供新功能。主要的科学贡献是开发了适用于多种化学品的路径预测模型、用于整体性能评估的专门评估方法以及用于用户特定性能估计的新颖的适用域算法。两个新数据集的引入以及 EC 类链接的创建使 enviPath 成为微生物生物转化研究中的独特资源。