enviPath – The environmental contaminant biotransformation pathway resource

TLDR

The University of Minnesota Biocatalysis/Biodegradation Database and Pathway Prediction System has been a unique resource for over 15 years, cataloguing microbial biotransformation pathways of xenobiotic chemicals. This paper presents enviPath, a complete redesign and reimplementation of UM‑BBD/PPS as the Environmental Contaminant Biotransformation Pathway Resource. enviPath builds on the UM‑BBD/PPS database, extends its coverage, allows user‑supplied data, incorporates relative reasoning and machine‑learning refinements, and offers a REST API and RDF backend for easy integration into workflows. enviPath is freely accessible at https://envipath.org, providing open access to its core data.

Abstract

The University of Minnesota Biocatalysis/Biodegradation Database and Pathway Prediction System (UM-BBD/PPS) has been a unique resource covering microbial biotransformation pathways of primarily xenobiotic chemicals for over 15 years. This paper introduces the successor system, enviPath (The Environmental Contaminant Biotransformation Pathway Resource), which is a complete redesign and reimplementation of UM-BBD/PPS. enviPath uses the database from the UM-BBD/PPS as a basis, extends the use of this database, and allows users to include their own data to support multiple use cases. Relative reasoning is supported for the refinement of predictions and to allow its extensions in terms of previously published, but not implemented machine learning models. User access is simplified by providing a REST API that simplifies the inclusion of enviPath into existing workflows. An RDF database is used to enable simple integration with other databases. enviPath is publicly available at https://envipath.org with free and open access to its core data.