enviPath

enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products. You can try it out below.

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News
  • Update - July 7, 2016

    We just deployed another update, most changes are on a lower level. Some important updates are: Introduction of multiple structures for one compound, updates in relative reasoning (more updates on this will come in the next month), introduction of a mapping servlet to map PPS rules to enviPath URIs, and many more. A changelog is given here.

  • Update and Publication - December 14, 2015

    We released another minor update that prepares the system for more biotransformation rules. Additionally, we fixed a bug that prevented the display of reviewed compounds in the system, all imported compounds from BBD should be visible again. In the next days, we will import another set of transformation rules. We are currently working on providing more return types for the system, as well as fixing existing bugs and preparing the system for the next steps. As always, if you notice any problems with enviPath, please tell us using the mailing list.

    A few weeks ago, our submission to NAR was published in the NAR early acces. It is available here. Please cite this paper when refering to enviPath:
    Wicker, Jörg; Lorsbach, Tim; Gütlein, Martin; Schmid, Emanuel; Latino, Diogo; Kramer, Stefan; Fenner, Kathrin enviPath - The Environmental Contaminant Biotransformation Pathway Resource. Nucleic Acid Research, 2015.

  • Migration from EAWAG-BBD/PPS to enviPath - November 5, 2015

    Another update to enviPath was just deployed. It consists mainly of smaller bugfixes and improvements in the user interface. We are still in the process of importing data from EAWAG-BBD/PPS to enviPath. The data from BBD (mostly pathways) are already fully imported, but we still are working on importing the biotransformation rules. Currently, we have 45 rules from PPS in enviPath. We will add a few more rules in the next days, and plan to have most of the rules imported in the next few months. The status of the migration from PPS to enviPath is shown here. The import of the rules is a long process, we have to export the rules from Chemaxon, and import them into the Ambit SMARTS/SMIRKS library. We use this process to evaluate the rules systematically and fix the problems we identify. If you notice any problems with a biotransformation rule (for example wrongly predicted reactions), please tell us using the mailing list.

  • Release - September 15, 2015

    We just released a new version of enviPath. Although there are still some minor known issues, this release can be considered as stable. This is the initial stable release, an overview of the features is given in our wiki. Feel free to contribute and upload your data.

    If you find any problems, or have any suggestions or questions please send an email or ontact us using the mailing list.

  • Update - August 21, 2015

    enviPath is close to a stable release, scheduled for September 15, 2015. Most functionality is already included into the system, and a large fraction of the data from the UM-BBD is already imported. In the next weeks until the stable release, the system will be updated more frequently.

    There are some known issues, we work on fixing them at the moment. Some of them are:

    • Internet Explorer / MS Edge is not fully supported
    • Text input on start page does not work, please use the draw function
    • Several minor problems when displaying scenarios

    If you find any problems, please send an email or contact us using the mailing list.

Latest Pathway

enviPath 101
  • Wiki

    The main documentation can be found in our wiki. We will add an introductory video and further documentation soon.