enviPathPlus – Fostering Interdisciplinary Sharing and Usage of Chemical Biodegradation Data

enviPath is an online platform dedicated to the biodegradation of chemicals in the environment. enviPath not only stores information on how microbes degrade chemical pollutants, but can also predict such biodegradation pathways using computational models.

In the enviPathPlus project, we are making enviPath more user-friendly and improving its connection to other resources for biochemical and genomic data. These enhancements will make it easier for researchers to share biodegradation data, provide stakeholders with important information to make decisions about the safety of chemicals, and help educate the next generation of scientists. With these enhancements, the knowledge and computational models in enviPath will hopefully contribute to the future development of chemicals that are safe and sustainable by design.

Understanding and predicting the fate of synthetic chemicals under different environmental conditions is essential to assess their potential risk to humans and ecosystems. The persistence of a chemical in the environment and the formation of transformation products are determined by the microbial reactions and enzymes involved in biodegradation.

enviPath is a unique resource that systematically stores biodegradation pathways, rates, and experimental conditions, and predicts pathways using expert and machine learning systems. The enviPathPlus project aims to improve the connection of the enviPath platform to two key research communities, namely systems biology and analytical chemistry, with the overall goal of improving the dialog between the different disciplines and providing a user-friendly platform for collaboration, data collection, exchange and integration.

Interdisciplinary collaboration between environmental and analytical chemists, microbiologists, bioinformaticians and systems biologists is key to a global understanding of biodegradation processes. Therefore, a first objective of enviPathPlus is to establish communication channels with key players in these fields to identify data and tool needs and to maintain an active exchange.

On a technical level, enviPathPlus aims to increase data exchange by making it easier for researchers to contribute data, and for users to download and integrate data and models into downstream tools. Regarding data contribution, user-friendly tools for data input are required to motivate analytical chemists performing biodegradation experiments to upload their data to enviPath. Downstream data usage can be facilitated by cross-referencing enviPath database entities with identifiers from other relevant (bio)chemical resources, and by providing biodegradation data in a standard format.

Finally, the enviPath platform needs to be easy-to-use and well-documented for both users of the user interface, as well as for scientists who wish to access enviPath data and tools programmatically.

To launch the enviPathPlus project, we organized a workshop on enviPath at the 2023 ICCE conference in Venice to promote enviPath as a resource to the environmental chemistry community, followed by a scoping workshop to gather the needs and ideas of key users and contributors. Through regular enviPath newsletters and social media updates, we encourage the scientific community to stay involved.

On a technical level, we have linked all compounds and reactions in enviPath to external key databases, and we now provide biodegradation pathways for download in an established standard format for data exchange in systems biology. We have also linked enviPath reactions to protein and gene sequences, which will facilitate the study and engineering of microbial communities capable of removing micropollutants.

To facilitate the interaction of analytical chemists with enviPath, we have developed an Excel spreadsheet containing all data elements to be reported for biodegradation studies in soil, activated sludge, and water-sediment systems, and we are promoting the use of this spreadsheet for data reporting in other projects (e.g., collection of PFAS degradation data). We have further improved the prediction of potential transformation products (TPs) by implementing a greedy search algorithm as the new default pathway search algorithm, and redesigned the user interface to facilitate the generation of predicted TPs for suspect screening in environmental samples.

Finally, we have redesigned the wiki of the enviPath website and documented theenviPath-python Application Programming Interface (API), which allows the seamless integration of enviPath into data analysis and modeling workflows.

By encouraging and facilitating data sharing in the interdisciplinary community of biodegradation research, we believe to have a significant impact in promoting Open Science practices in the field.