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Nucleic Acids Res. 2016 Jan 4;44(D1):D502-8. doi: 10.1093/nar/gkv1229. Epub 2015 Nov 17.

enviPath--The environmental contaminant biotransformation pathway resource.

Author information

1
Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, 55128 Mainz, Germany wicker@uni-mainz.de.
2
Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, 55128 Mainz, Germany.
3
Scientific IT Services, ETH Zürich, Weinbergstrasse 11, 8092 Zürich, Switzerland.
4
Department of Environmental Chemistry, Eawag, Überlandstrasse 133, 8600 Dübendorf, Switzerland.
5
Department of Environmental Chemistry, Eawag, Überlandstrasse 133, 8600 Dübendorf, Switzerland Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland.

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.

PMID:
26582924
PMCID:
PMC4702869
DOI:
10.1093/nar/gkv1229
[Indexed for MEDLINE]
Free PMC Article

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