enviPath - The environmental contaminant biotransformation pathway resource

被引：119

作者：

Wickert, Joerg ^{[1
]}

Lorsbach, Tim ^{[1
]}

Guetlein, Martin ^{[1
]}

Schmid, Emanuel ^{[2
]}

Latino, Diogo ^{[3
]}

Kramer, Stefan ^{[1
]}

Fenner, Kathrin ^{[3
,4
]}

机构：

[1] Johannes Gutenberg Univ Mainz, Inst Comp Sci, Staudingerweg 9, D-55128 Mainz, Germany

[2] ETH, Sci IT Serv, Weinbergstr 11, CH-8092 Zurich, Switzerland

[3] Eawag, Dept Environm Chem, Uberlandstr 133, CH-8600 Dubendorf, Switzerland

[4] ETH, Dept Environm Syst Sci, CH-8092 Zurich, Switzerland

来源：

NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / D1期

基金：

瑞士国家科学基金会;

关键词：

PREDICTION; METABOLISM; KNOWLEDGE; FATE;

D O I：

10.1093/nar/gkv1229

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The University of Minnesota Biocatalysis/Biodegrad ation 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.

引用

页码：D502 / D508

页数：7

共 20 条

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