enviPath – The Environmental Contaminant Biotransformation Pathway Resource

Jörg Wicker, Tim Lorsbach, Martin Gütlein, Emanuel Schmid, Diogo Latino, Stefan Kramer, Kathrin Fenner (2016): enviPath - The Environmental Contaminant Biotransformation Pathway Resource. In: Nucleic Acid Research, 44 (D1), pp. D502-D508, 2016.

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.

BibTeX (Download)

@article{wicker2016envipath,
title = {enviPath - The Environmental Contaminant Biotransformation Pathway Resource},
author = {J\"{o}rg Wicker and Tim Lorsbach and Martin G\"{u}tlein and Emanuel Schmid and Diogo Latino and Stefan Kramer and Kathrin Fenner},
editor = {Michael Galperin},
url = {http://nar.oxfordjournals.org/content/44/D1/D502.abstract},
doi = {10.1093/nar/gkv1229},
year  = {2016},
date = {2016-01-04},
journal = {Nucleic Acid Research},
volume = {44},
number = {D1},
pages = {D502-D508},
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. },
keywords = {biodegradation, cheminformatics, computational sustainability, enviPath, linked data, metabolic pathways, multi-label classification},
pubstate = {published},
tppubtype = {article}
}