UM-BBD User Survey Comments

Comments on the UM-BBD User Survey
April 20, 2000

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Comments were received from 15/50 (30%) of the respondents to the survey, slightly higher than last year. These were edited to remove personal identifying information and are collected here. We answered a few of the comments; our comments are indicated by >.
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We would like to learn more about the biodegradion of hydrocarbon mixtures.
> We do not cover mixtures or polymers in this database.  
> You may find useful information in the Bioremediation Discussion Group 
> (http://biogroup.gzea.com/).
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Reinforce the research about PBC's compound remediation
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It will be great if the description of enzyme properties include the full method description for assayng the enzyme activity or correct reference on that method.
> While we do not have this information specifically on our page, we do
> have a link to one primary reference for each reaction and a link
> to a search of Medline which might have the information you desire.
>
> The BRENDA database (http://www.brenda.uni-koeln.de:80/) does contain 
> this information for all enzymes which have been assigned full 
> four-digit EC codes.  A link to BRENDA is found on UM-BBD pages
> for such enzymes.
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Thank you for your excellent organization to see these pathways and compounds
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I am well aware that phenol degrades under both anaerobic and aerobic pathways, but your database does not include the aerobic pathway. Need more pathways for specific compounds.
> Our pathway map for anaerobic phenol used to state "An aerobic phenol
> degradation pathway is shown in the phenylalanine metabolism map in 
> the Kyoto Encyclopedia of Genes and Genomes (KEGG)."  But due in part
> to your comment, we have added the initial aerobic phenol biodegradation
> reaction to our Nitrobenzene Pathway Map.
>
> Not all compounds for which the UM-BBD contains biodegradation information 
> have named pathways; use our Search function or browse the lists of 
> information found on the Search page.
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Thank you for your works in UM-BBD and for all the information we can find in the data base. Thank you very much for your help.
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This is a very well run site!
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would be nice if an internet search for a chemical (by name or CAS#) yielded hits on your site. 
> Depending on which search engine you use, this may be already true.
> If you try Google (http://www.google.com/) to search
> (for example) for toluene, atrazine, or napthalene, the UM-BBD 
> pathway page is first or second in the list of thousands of hits
> found for each search.
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1. Include all the basic cellular pathways and cellular metabolism, like Krebs cycle, Pentose shunt, all synthetic and degragative pathways that would be in a basic biochemistry book, as well as the "exotic" pathways that you have.
> We try not to duplicate the work of others, and several excellent
> databases already cover basic cellular pathways common to most
> organisms.  For example, see the Kyoto Encyclopedia of Genes and 
> Genomes, (http://www.genome.ad.jp/kegg/kegg.html).
2. Put more info on each page, so one does not have to flip to so many different pages to see each detail of the reactions and structures, or make this an option.
> This functionality is available on our mirror site in the UK,
> hosted on the European Bioinformatics Institute's SRS server
> (http://srs.ebi.ac.uk/).
>  
> From a complete list of UCOMPOUND, UENZYME, UREACTION, or UPATHWAY, 
> or any search of these databanks, you can select as many entries  
> as you want and have all of them appear on one web page.
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We find this to be a useful resource that facilitates investigative operations with a quick reference capability which in most situations has provided informative directions.
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This is a fantastic resource. Keep up the execellent work.
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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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I think that this is a great service. I am not sure how, but I think it would be useful to encourage experts to contribute comments including corrections to the database.
> The UM-BBD contains the contributions of many experts.  Their names
> are listed in the Contributor's Page.  We encourage such contributions; 
> please contact us.
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The potential of toluene production from the degradation of lignin during secondary treatment in a Aerated Stablization Basin. The lignin is released from production of pulp using Aspen trees.
> If you can give us any references to this, we would be happy to add 
> them to the narrative part of our toluene pathway map.
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Pathways are not exhaustive. There is no pathway for the degradation of lignin available. The enzyme etherase is not found in the enzyme search. Many more pathways has to be added. Specialists in the fields should be listed and they should be encouraged to contribute to the database.This will help researchers worldover. This database is a useful resource which caters to the needs of a lot of people and congrtatulations for the efforts put in.
> Please let us know of suggested additions to existing pathways. 
> 
> We do not include polymers such as lignin in the database.
> We do have a link to Lignin Biodegradation by White Rot Fungi from 
> Wageningen Agricultural University, The Netherlands on our 
> Useful Internet Resources page.
>
> "Ether hydrolase" (EC 3.3.2.), not "etherase", is the official name for
> that class of enzymes. The UM-BBD contains 7 reactions catalyzed by 
> enzymes with that code.
>
> As stated above, we encourage contributions by specialists; 
> please contact us.
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