UM-BBD User Survey Comments

Comments on the UM-BBD User Survey
April 12, 2001

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Comments were received from 15/60 (25%) of the respondents to the survey, about the same as last year. These were edited to remove personal identifying information and are collected here. We have made a few comments ourselves; our comments are indicated by >.
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Saxitoxin and Anatoxin-a, both created by Cyanobacteria, both deadly neurotoxins. I would like to know how to biologically break them down.
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Reaction mechanisms such as in apoptosis by oxidant/reductant radicals.
> The UM-BBD contains selected enzymatic reaction mechanisms, though not
> that particular one, which is a bit out of our area.  The ones it does
> contain are listed in the Graphics Index.
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communication networks within working groups around the world, projects, collaboration possibilities, educational opportunities, biotransformation challenges... techniques....
> We try not to duplicate functions that are available elsewhere.
> Some of your concerns are met in the Bioremediation Discussion Group 
> (http://www.bioremediationgroup.org/).
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How are things going with the link that John Urbance and Jim Tiedje wanted to make between the BBD and their proposed Biodegradative Strain Database? It would truly be grand to have a meta-database that would allow researchers to get info on pathways as well as the organisms in which the pathways occur, and the phylogenetic distribution of these pathways.
> The Biodegradative Strain Database (BSD) is alive and well at
> http://bsd.cme.msu.edu/.
> 
> At present it contains 133 substrates.  Since it includes substrates
> even if their detailed biodegradation pathways are not known, not all of 
> them are included in the UM-BBD's 650+ compounds.  Its substrate pages 
> contain links to UM-BBD compound pages where possible.  We plan to link
> UM-BBD compound pages to the BSD as time permits.  However, because of 
> their different inclusion criteria, there will never be complete
> overlap between the two databases.
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You are doing a great job.
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I think it is a wonderful site and wish there was more info like this out on the web. I also wish that the database could be expanded to include more compounds.
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This is a very useful and unique resource. Keep up the great work. I would like to see more information about polymer biodegradation as this is my area of interest.
> We do not cover polymers or mixtures in this database.  
> You may find useful information in the Bioremediation Discussion Group 
> (http://www.bioremediationgroup.org/).
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We appreciate your useful informations. We hope more development of your works.
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KEEP ON WITH THIS GREAT JOB. THANKS FOR ALL YOUR TIME AND EFFORT
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I wish to express my thanks to developers of UMBBD for maintainance of this useful source of information.
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information relating the pathway and/or microbes to enviromental fate and human health
> For more information on pathway or reaction significance, check the 
> literature references for each UM-BBD reaction.  For more information 
> on individual microbes, check the links to the ATCC or DSMZ found 
> through the organism name on pathway maps or the Microorganism Index.
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a short comment: it would be helpful to get an idea about the significance / functionality of pathways presented in the database. Thats certainly difficult, I know. Maybe one could make a difference between biochemical reactions which were shown and pathways which were analysed as such (stoichiometric turnover, intermediates etc).
> For more information on pathway or reaction significance, check the
> literature references for each UM-BBD reaction.  In general UM-BBD
> pathways are based on papers which report two or more reactions
> of a "real" pathway.  We often mention these papers in the narrative 
> on a pathway map.  We then search the literature for additional 
> references for individual reactions.  Such references are usually 
> not the basis for an entire pathway.
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Many thanks
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Pathways presented at various levels providing more in-depth information for those who require, perhaps as links to related areas such as toxicology.
> Unfortunately, our limited resources do not permit us to expand the
> depth of our information in this way.  For several years now, the
> majority of our users have stated that, given a choice, they would 
> prefer us to increase breadth (more pathways) rather than depth
> (more functions for existing pathways).
>
> You may be interested in the EcoCyc Database, which provides several
> different levels of pathway information for metabolic pathways 
> found in E. coli.  http://ecocyc.org/
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On the behalf of all the users, I take the liberty of congratulating you on your work and wish you, Dr. Wackett and the UMBBD team a bright future. I hope more number of new users will get to know the excellence of this resource database.
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