enviPath - How to Cite

If you use enviPath in your research, please cite our work. Citations help us demonstrate the impact of our platform and support continued development and maintenance.

Quick Reference

The citation depends on which specific tools or models you used. Please cite the relevant publications below.

Main Platform Citation

If you use the enviPath platform in general, please cite:

Advancements in biotransformation pathway prediction: enhancements, datasets, and novel functionalities in enviPath

Authors: Hafner, J., Lorsbach, T., Schmidt, S., Brydon, L., Dost, K., Zhang, K., Fenner, K., and Wicker, J.
Journal: Journal of Cheminformatics, 16(1), 93
Year: 2024
DOI: 10.1186/s13321-024-00881-6

Show BibTeX

@ARTICLE{Hafner2024,
title     = "Advancements in biotransformation pathway prediction:
                enhancements, datasets, and novel functionalities in enviPath",
author    = "Hafner, Jasmin and Lorsbach, Tim and Schmidt, Sebastian and
                Brydon, Liam and Dost, Katharina and Zhang, Kunyang and Fenner,
                Kathrin and Wicker, J{\"o}rg",
journal   = "J. Cheminform.",
publisher = "Springer Science and Business Media LLC",
volume    =  16,
number    =  1,
pages     = "93",
month     =  aug,
year      =  2024,
doi       = "10.1186/s13321-024-00881-6"
}

Pathway Prediction System

If you use the pathway prediction functionality, please also cite:

Predicting Biodegradation Pathways Using a Hybrid Relative Reasoning Model

Authors: Wicker, J., Fenner, K., Ellis, L., Kramer, S.
Journal: Biotechnology and Bioengineering, 110(3), 837-846
Year: 2013
DOI: 10.1002/bit.24744

Show BibTeX

@article{wicker2013predicting,
  title={Predicting biodegradation pathways using a hybrid relative reasoning model},
  author={Wicker, J{\"o}rg and Fenner, Kathrin and Ellis, Lynda and Kramer, Stefan},
  journal={Biotechnology and Bioengineering},
  volume={110},
  number={3},
  pages={837--846},
  year={2013},
  publisher={Wiley Online Library},
  doi={10.1002/bit.24744}
}

Machine Learning Models

enviPath-Transformer (Latest ML Model)

If you use the Transformer-based prediction model, please cite:

Authors: Brydon, L., Zhang, K., Dobbie, G., Taškova, K., and Wicker, J.
Journal: Journal of Cheminformatics, 17(1), 21
Year: 2025
DOI: 10.1186/s13321-025-00969-7

Relative Reasoning Models

For relative reasoning and machine learning approaches:

Authors: Fenner, K., Gao, J., Kramer, S., Ellis, L., Wackett, L.
Journal: Environmental Science & Technology, 42(15), 5761-5767
Year: 2008
DOI: 10.1021/es800408g

Package-Specific Citations

If you use data from a specific package within enviPath, please also acknowledge the package creators and cite any relevant publications associated with that package. Package-specific citation information is available on each package's detail page.

Example Acknowledgment Text

You may use the following text in your acknowledgments section:

"Biotransformation pathway predictions were performed using enviPath (https://envipath.org), a database and prediction system for microbial biotransformation of organic environmental contaminants."

Additional Resources

For a complete list of publications related to enviPath, please visit:

Thank You!

Thank you for citing enviPath. Your citations help demonstrate the impact of our work and enable us to continue providing this resource to the scientific community.

Questions?

If you're unsure which papers to cite or have questions about citations, please contact us or ask on our community forums.