Differences

This shows you the differences between two versions of the page.

--- start [2024/08/14 10:00] – [Data Upload] strich
+++ start [2025/02/18 15:24] (current) – [Data Upload] strich
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 ======Main Page======
-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 |}}
+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.
+{{map>timeline_static1.png?1000|Timeline of enviPath}}
+    * [[https://academic.oup.com/nar/article/38/suppl_1/D488/3112190|Link to Gao et al 2009 @80,100,350,205|target=_tab]]
+    * [[https://academic.oup.com/nar/article/44/D1/D502/2502710?login=true|Wicker et al 2016 @370,100,660,200|target=_tab]]
+    * [[https://pubs.rsc.org/en/content/articlelanding/2017/em/c6em00697c|Latino et al 2017 @500,325,765,444|target=_tab]]
+{{<map}}
 ====Database====
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 ==== Data Upload ====
-We are working to upload biotransformation pathways in a quick and efficient manner using an excel workbook. If you want to add your data to a future reviewed package, please fill out this template {{ :envipath_upload_template_july2024.xlsx |}} and upload your completed version to our [[https://www.dropbox.com/scl/fo/9hs9cjf27ezu690yg15vt/AFwci9ls8xoGEWnv5wlMf38?rlkey=vfjvw3wga4qtap53m7sijad8e&st=trhvvtrc&dl=0|Dropbox folder]]. Note- when you upload your filled-out version, you will need to rename it to something unique (i.e. lastname_firstname_yymmdd_compoundname.xlsx)
+We are working to upload biotransformation pathways in a quick and efficient manner using an excel workbook. If you want to add your data to a future reviewed package, please fill out this template {{ :envipath_upload_template_2025.xlsx |}} and upload your completed version to our [[https://www.dropbox.com/scl/fo/9hs9cjf27ezu690yg15vt/AFwci9ls8xoGEWnv5wlMf38?rlkey=vfjvw3wga4qtap53m7sijad8e&st=trhvvtrc&dl=0|Dropbox folder]]. Note- when you upload your filled-out version, you will need to rename it to something unique (i.e. lastname_firstname_yymmdd_compoundname.xlsx)
+==== Associated Resources ====
+[[https://github.com/MSM-group/ContaHMM?tab=readme-ov-file#contahmm-a-resource-for-the-search-of-biotransformation-related-bacterial-genes|ContaHMM: A Resource for the search of Biotransformation-Related Bacterial Genes]]
+We present a dataset and HMMs (Hidden Markov Models) for biotransformation-related bacterial genes, compiled from existing databases and enhanced by extensive metadata collection, manual curation, and HMM generation.This collection aims to facilitate the annotation of biotransformation-related enzymes and expand the known examples in the field.