EnviPath--The environmental contaminant biotransformation pathway resource.

Jörg Wicker,Emanuel Schmid,Diogo Latino,Stefan Kramer,Kathrin Fenner,Martin Gütlein,Tim Lorsbach

doi:10.1093/nar/gkv1229

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.

Highlights

EnviPath is the successor of the University of Minnesota Biocatalysis/Biodegradation Database and Pathway Prediction System (UM-BBD/PPS)
The UM-BBD/PPS was recently transferred to Eawag and renamed to EAWAGBBD/PPS
EnviPath is a new system for microbial biotransformation pathways. This system is the successor of EAWAG-BBD, and includes the data from EAWAG-BBD, a thoroughly curated and unique data set

Summary

INTRODUCTION

EnviPath is the successor of the University of Minnesota Biocatalysis/Biodegradation Database and Pathway Prediction System (UM-BBD/PPS). EnviPath contains all data in terms of reactions, compounds, pathways and transformation rules from the EAWAG-BBD. One of the major differences of enviPath compared to its previous implementation, EAWAG-BBD/PPS, is its openness and flexibility This system can be filled with data by every user or research group. Users can create packages with their researched pathways and later publish the data set on enviPath openly. Research groups can be established as groups and collaborate on their data Another advantage of a registered user is the possibility to establish default settings for most operations, e.g. the list of packages to use for pathway prediction or browsing the database. Certain packages are selected for each user, but registered users can change this list and use different transformation rules for pathway predictions by default. The package is publicly accessible and can be referred to via the URL and downloaded

RELATED WORK

CONCLUSION AND FUTURE