What's New in the EAWAG-BBD?

January 18, 2016
The successor system of Eawag-BBD/PPS is getting up to speed. enviPath has been first released on September 15, 2015, and a first article on its functionalities has been published in the 2016 Database Issue of Nucleic Acids Research. enviPath - The Environmental Contaminant Biotransformation Pathway Resource - is a complete redesign and reimplementation of Eawag-BBD/PPS. On the database side, we have imported the entire database from Eawag-BBD/PPS as a basis. Besides this, one of the strengths of enviPath lies in offering users the possibility to start building their own databases with biotransformation data and integrating it with Eawag-BBD data, if wanted. On the prediction side, different relative reasoning models are implemented, including rule-based relative reasoning and previously published, but not implemented machine learning models. However, their use is currently still hampered by slow progress in translating the Eawag-PPS biotransformation rules from proprietary format into open source SMIRKS format. Progress with rule transformation is reported here.
User access is simplified by providing a REST API that simplifies the inclusion of enviPath into existing workflows. An RDF database is used to enable simple integration with other databases. enviPath is publicly available with free and open access to its core data.
We are also working on developing a new database DAR soil with all pesticide soil biodegradation pathways freely available through EFSA Draft Assessment reports. These data will be made gradually publically available, with the complete data set release expected in mid-2017.
For now, we encourage you to try out and start familiarizing yourself with the functionalities of enviPath. We also encourage you to subscribe to the enviPath mailing list and use it to send us any kind of feedback on the system.

June 30, 2014
As of July 1, 2014, all rights of UM-BBD/PPS will be transferred to Eawag. For this reason, we have moved the existing system to a new server (http://eawag-bbd.ethz.ch) and renamed it as EAWAG-BBD. Please update your bookmarks accordingly. Users entering through the old URL will be re-directed to the new server for a period of 6 months. The Contributors page has been updated to reflect the above changes. Lynda Ellis, University of Minnesota, has been moved to International Scientific Advisory Board and Former Staff.

April 7, 2014
We would like to share some exciting news with you! In February 2014, we have been informed that a 3-year project for the further development of UM-BBD/PPS has been approved for joint funding by the Swiss National Science Foundation (SNSF) and the Deutsche Forschungsgemeinschaft (DFG). The project will be carried out between the research groups of Dr. Kathrin Fenner at Eawag in Switzerland and Dr. Stefan Kramer at the Johannes Gutenberg University in Mainz. Scientific IT Services at ETH Zürich will further support the project.
The main goal of the project is to develop a next-generation system for the accurate prediction of microbial biotransformation pathways and half-lives under different, environmentally relevant conditions. For this, we will also renew the database and system architecture towards a more flexible and interactive system that can be interfaced with other existing data resources. In short, it should not only become easier for you to enter your own, experimentally explored biotransformation pathways, but it should also be possible to more easily link pathway predictions into your workflows for chemical risk assessment or analytical chemistry. Stay tuned!
Because we are currently focusing all our resources on preparing the transition to the new system, a first public version of which we hope to release towards late 2014, we are not actively adding any new pathways to the current system. Behind the scenes we are, however, starting to add pesticide soil biodegradation pathways into the new system, the first of which will be made publically available as package in the new system in late 2014.

October 11, 2013
A new pathway for the degradation of the fungicide benomyl was added, which has been contributed by Lynda Ellis and Michael Turnbull, University of Minnesota.
The nitrophenol family pathway was revised to include a new enzyme that transforms 4-nitrocatechol into 2-hydroxy-1,4-benzoquinone in accordance with IUBMB.
ChemAxon was upgraded from version 5.4 to 5.12 and two rules (bt0330 and bt0342) were re-written to work properly under the updated version.

May 15, 2013
The EBI Mirror of the UM-BBD Database on SRS@EMBL-EBI is being retired by the end of May 2013. Links to EBI mirror pages have been removed from this web site.

April 14, 2013
A new pathway for the degradation of the human pharmaceutical diazepam by funghi was added which had been contributed by Lynda Ellis and Michael Turnbull, University of Minnesota.
The nicotine pathway was revised to include two enzymes that transform 4-(methylamino)-butyrate in accordance with IUBMB.
On the Links page, a link to "Enzymes with a reaction scheme" on the website of the International Union of Biochemistry and Molecular Biology (IUBMB) has been added in the "Enzymes and their Genes" section.

December 7, 2012
Two pathways were added: A pathway for the b-blocker pharmaceutical atenolol in activated sludge consortia, contributed by Kathrin Fenner, Eawag, and a pathway for the organophosphorous insecticide triazophos in pure culture, contributed by Lynda Ellis and Michael Turnbull, University of Minnesota.
The page Systematic List of UM-BBD Pathways is no longer supported and its link was removed from the Search page. On the Links page, the link to the Biodegradative Strain Database at Michigan State University was deleted. Instead, a link to Straininfo has been added in the Microorganisms Section.

September 28, 2012
The pathway for the polyaromatic hydrocarbon (PAH) compound acenaphthylene, was updated by adding a parallel pathway for the close structural analogue acenaphthalene. This pathway was updated by Lynda Ellis.
The database and pathway prediction system is now hosted on our ETHZ mirror, which has taken over primary hosting duties since June, 25. Currently, all old URLs are redirected to ETH and therefore will continue to work for a while. However, we suggest that you update them as soon as you can by changing all umbbd.msi.umn.edu URLs to umbbd.ethz.ch . Along with the move of the server, the email list has also moved to a new server. To subscribe, unsubscribe, or change your subscription options, go to: https://sympa.ethz.ch/sympa/subscribe/umbbd-users.
On the Links page, the link for Hazardous Substances Information System from the Australian Safety and Compensation Council was updated, and the link for OxDbase was deleted.

May 15, 2012
A pathway for nitrate (anaerobic), a source of nitrogen for growth and possible electron sink, has been added. This pathway was contributed by a student from Manchester College, Indiana, under direction of his instructor, Jeffery P. Osborne. You may have noticed the long downtime of our Minnesota server last month. We apologize for this unscheduled outage. We are moving to a new server, and hope these problems will decrease in the coming months. The new server is presently our ETHZ mirror, and will take over primary hosting duties within 30 days, exact time not known yet. The change should be transparent to users. However, What's New entries will be less frequent at first. The move will mean all umbbd.msi.umn.edu URLs will change to umbbd.ethz.ch . The old URLs will continue to work for a while, but update them as soon as you can. Along with the move of server, the email list will also be moving. The move of email server should also be transparent to users. Watch for a message announcing the change in the coming months. The Contributors page has been updated to reflect the above changes. Kathrin Fenner, EAWAG, and Emanuel Schmid, ETHZ, have been added to "Staff." Also, Jeffrey P. Osborne, Manchester College, Indiana, USA, has been added to the International Scientific Advisory Board. On the Links page, the link for Scorecard was updated, and the link for GREP: Generator of Reaction Equations and Pathways was deleted.

April 20, 2012
A pathway for iminodisuccinate, a metal chelator, has been added, and the pathway for camphor, has been updated. The iminodisuccinate pathway was contributed by students from Manchester College, Indiana, under direction of their instructor, Jeffery P. Osborne. This pathway has been added to the UM-BBD list of metals, metalloids and metal chelators. A list of external links found on UM-BBD text pathway maps has been created. The wide diversity of information sources used in these web pages is of interest. This list also helps UM-BBD developers keep these links current. Macintosh users who apply the Java for OS X Lion 2012-003 update will find that it disables Java applets. Java applets are used in the UM-PPS and the search for chemical structures in the UM-BBD. Enable Java applets if you wish to use those functions.

March 26, 2012
Pathways for the starch oligomer, a polymer of glucose in which the monomers are connected via an alpha-1,4 glucosidic bond, and fungal 1,5-anhydro-D-fructose, a starch metabolite, and an update to the pathway for methyl-tert-butyl ether, have been added. The two starch pathways were contributed by a student from Manchester College, Indiana, under direction of her instructor, Jeffery P. Osborne. The UM-BBD is 17 years old now, almost an adult. A picture from its 2012 birthday party has been added to the bottom of the photo gallery page.

March 1, 2012
A pathway for acenaphthylene, a bridged polyaromatic hydrocarbon, and an update to the pathways for benzoate, and alachlor, have been added. One new reaction mechanism graphic has been added, for the hydrolysis of 2,3-epoxybenzoyl-CoA to 3,4-dehydroadipyl-CoA semialdehyde in the benzoate pathway. This brings the number of such graphics to 36. A list of all reaction mechanism graphics is available. A new publication is available: Ellis LB, Wackett LP. (2012) "Use of the University of Minnesota Biocatalysis/Biodegradation Database for study of microbial degradation" Microbial Informatics and Experimentation 2: 1. A link to the full text is available on the Publications page. The ability to see compound and reaction graphics are in displayed pathways is now found on the ETHZ UM_BBD mirror. For example, see the displayed pathway for the glyphosate dehydrogenase reaction, and hold the mouse over the glyphosate oval. In the Links page, a link for Publications from the Canadian Network of Toxicology Centers was deleted. The What's New page restarts; 2011 activities have been archived.

January 17, 2012
Pathways for atropine, and cocaine, structurally-related pharmaceuticals, have been added. The cocaine pathway was contributed by a student from Manchester College, Indiana, under direction of her instructor, Jeffery P. Osborne. A "Display a Pathway" link is found at the bottom of each reaction page. When clicked, it displays in graphical form a pathway of all UM-BBD reactions starting from the chosen reaction. Now when a user moves the mouse to a compound oval or reaction name in a displayed pathway and pauses, an image of the compound or reaction is displayed. For example, see the displayed pathway for the glyphosate dehydrogenase reaction, and hold the mouse over the glyphosate oval. A help page for displayed pathways is available. The code for this is based on code for a similar function found in KEGG pathway maps. This function is not yet avavailable on the ETHZ UM-BBD. The ETHZ UM-PPS mirror, originally 4 times slower, now is even faster than the UM UM-PPS. Check it out! We will run a short "load test" on this server during the week of Jan 23. For a few hours on one day of that week (not yet decided), we will divert all UM-PPS traffic to the ETHZ UM-PPS, to test whether it can handle this load and serve as backup when the UM UM-PPS is down.

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