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| ======Main Page====== | ======Main Page====== |
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| enviPath is an online, publically available database and prediction system for microbially mediated biotransformations of organic environmental contaminants. It is the successor of the University of Minnesota Biocatalysis/Biodegradation Database and Pathway Prediction System (now [[http://eawag-bbd.ethz.ch/|EAWAG-BBD/PPS]]) and is a continually evolving product of over 20 years of international scientific collaboration. The enviPath platform provides a thorough, mechanistic understanding and prediction of biotransformation pathways and rates in different experimental and environmental conditions such that academic research teams, consultants, public authorities, and chemical industries can collectively work to reduce harmful chemical contamination in the environment. | enviPath is an online, publically available [[start#database]] and [[start#prediction]] system for microbially mediated biotransformations of organic environmental contaminants. It is the successor of the University of Minnesota Biocatalysis/Biodegradation Database and Pathway Prediction System (now [[http://eawag-bbd.ethz.ch/|EAWAG-BBD/PPS]]) and is a continually evolving product of over 20 years of international scientific collaboration. The enviPath platform provides a thorough, mechanistic understanding and prediction of biotransformation pathways in different experimental and environmental conditions such that academic research teams, consultants, public authorities, and chemical industries can collectively work to reduce harmful chemical contamination in the environment. Below is a brief timeline describing the history of enviPath.{{ :timeline_static1.png?1000 |}} |
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| ====Database==== | ====Database==== |
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| | Biotransformation pathways reported in scientific literature as well as predicted or user-entered pathways can all be stored on the database provided within the enviPath platform. You can browse information in the database using the menu on the top banner of [[https://envipath.org/|start page]]. The enviPath database is organized into packages, where a user can select which data to access by specifying the package that is most relevant for his/her specific purpose. Each package has an owner who can grant reading or writing permissions. We list data only as reviewed if it is reviewed by one of the organisations or groups in the reviewer group. |
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| The enviPath database stores reviewed pathways from scientific literature and predicted or user-entered pathways. You can browse information in the database using the menu on the top banner of [[https://envipath.org/|start page]]. The database is organized in packages. Each package has an owner who can grant reading or writing permissions. We list data only as reviewed if it is reviewed by one of the organisations or groups in the reviewer group. | |
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| //Additional literature related to enviPath is listed here// | //Additional literature related to enviPath is listed here// |
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| Gao, J., Ellis, L. B. M., & Wackett, L. P. (2009). The University of Minnesota Biocatalysis/Biodegradation Database: Improving public access. Nucleic Acids Research, 38(SUPPL.1), 488–491. [[https://doi.org/10.1093/nar/gkp771]] | * Gao, J., Ellis, L. B. M., & Wackett, L. P. (2009). The University of Minnesota Biocatalysis/Biodegradation Database: Improving public access. Nucleic Acids Research, 38, 488–491. [[https://doi.org/10.1093/nar/gkp771]] |
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| Trostel, L., Coll, C., Fenner, K., & Hafner, J. (2023). Combining predictive and analytical methods to elucidate pharmaceutical biotransformation in activated sludge. Environmental Science: Processes and Impacts, 25(8), 1322–1336. [[https://doi.org/10.1039/d3em00161j]] | |
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| Hafner, J., Fenner, K., & Scheidegger, A. (2023). Systematic Handling of Environmental Fate Data for Model Development─Illustrated for the Case of Biodegradation Half-Life Data. Environmental Science & Technology Letters, 10(10), 859–864. [[https://doi.org/10.1021/acs.estlett.3c00526]] | * Trostel, L., Coll, C., Fenner, K., & Hafner, J. (2023). Combining predictive and analytical methods to elucidate pharmaceutical biotransformation in activated sludge. Environmental Science: Processes and Impacts, 25(8), 1322–1336. [[https://doi.org/10.1039/d3em00161j]] |
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| | * Hafner, J., Fenner, K., & Scheidegger, A. (2023). Systematic Handling of Environmental Fate Data for Model Development─Illustrated for the Case of Biodegradation Half-Life Data. Environmental Science & Technology Letters, 10(10), 859–864. [[https://doi.org/10.1021/acs.estlett.3c00526]] |
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| | * Hafner, J., Lorsbach, T., Schmidt, S., Brydon, L., Dost, K., Zhang, K., Fenner, K., & Wicker, J. S. (2023). Advancements in Biotransformation Pathway Prediction: Enhancements, Datasets, and Novel Functionalities in enviPath. [[https://doi.org/10.21203/rs.3.rs-3607847/v1]] |
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| | * Zhang, K., & Fenner, K. (2023). enviRule: an end-to-end system for automatic extraction of reaction patterns from environmental contaminant biotransformation pathways. Bioinformatics, 39(7). [[https://doi.org/10.1093/bioinformatics/btad407]] |
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| ==== Documentation==== | ==== Documentation==== |
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| * [[Packages]] | |
| * [[Pathways]] | |
| * [[Pathway Prediction]] | |
| * [[Rules]] | |
| * [[Compounds]] | * [[Compounds]] |
| * [[Reactions]] | * [[Reactions]] |
| * [[Relative Reasoning]] | * [[Rules]] |
| | * [[Pathways]] |
| * [[Scenarios]] | * [[Scenarios]] |
| | * [[Packages]] |
| | * [[Pathway Prediction]] |
| | * [[Relative Reasoning]] |
| * [[Settings]] | * [[Settings]] |
| * [[Searching Function]] | * [[Searching Function]] |
