Client for the 'enviPath' 'RESTful' API

The environmental pathway database ('enviPath') is a key resource for the functional annotation and pathway prediction of microbial communities, providing knowledge on biotransformation pathways along with the chemical reactions and produced compounds. This package enables the programmatic access to 'enviPath' by porting the database 'RESTful' API from R. This includes methods to both retrieve entries and predict pathways for custom compounds.

enviPathR: the R Client for the enviPath RESTful API

This package provides a client to the enviPath biotransformation database and pathway prediction system. It accesses enviPath resources through its legacy API. A new, faster API is currently under development.

Installation

CRAN release version:

install.packages("enviPathR")

Beta version:

remotes::install_github("enviPath/enviPathR")

Terms of use

While enviPathR itself is openly available under an Artistic 2.0 license, the enviPath database and pathway prediction system is freely accessible only for academic use. More information on scope of use and commercial licensing can be found in the enviPath terms of use.

References

If you use enviPath in your research please cite:

• Hafner, J., Lorsbach, T., Schmidt, S., Brydon, L., Dost, K., Zhang, K., Fenner, K., & Wicker, J (2024). Advancements in Biotransformation Pathway Prediction: Enhancements, Datasets, and Novel Functionalities in enviPath. Journal of Cheminformatics, 16, 93, https://doi.org/10.1186/s13321-024-00881-6

• Wicker, J., Lorsbach, T., Gütlein, M., Schmid, E., Latino, D., Kramer, S., & Fenner, K. (2016). enviPath - The environmental contaminant biotransformation pathway resource. Nucleic Acids Research, 44(D1), D502–D508. https://doi.org/10.1093/nar/gkv1229