enviPath--The environmental contaminant biotransformation pathway resource

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.

Figure 1.

Diagram of the enviPath entities, the navigation possibilities between them and their display on screen (note that the figure does not display all logical relationships between the entities from the data model or a flow chart of the actual pathway prediction with inputs and outputs of computations). On the most left, user input is given via the web form in a visual editor or via SMILES input. From this input, a pathway is predicted using the Prediction Engine and truncation strategy. Alternatively, if a pathway for that compound is already stored, the stored pathway from the database is shown. Note that here we show an example from the database, not an actual predicted pathway. The pathway is linked to Reactions (on the edges) and Compounds (on the nodes). A Reaction is further linked to the Rule by which it is predicted. In the case of manually inserted Reactions, links to Rules can be present and set; in this case, the links explain from which Reaction the Rule is generalized. Furthermore, additional information is stored with all entities, named Scenario. An example is shown in the figure, in which the additional information of the Reaction, the link to the corresponding Pubchem entry and the enzyme involved in the reaction is displayed. Furthermore, every entity is organized in a Package.