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Biocatalysis/Biodegradation Database

Reviewed:	Jul 23, 2002 by Biology Editorial Board
Overview:	Housed at the University of Minnesota, this database provides access to details of microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds such as environmental pollutants. Pathway maps are interactive and clicking on compounds provides access to more information about the metabolic role of the compound. Data can also be accessed about specific enzymes, or specific microorganisms. A recent update (2002) is an animated reaction. The site is kept current and users can learn of recent additions linking to the monthly update titled "What's New?".
Learning Goals:	To provide information on microbial enzyme-catalyzed reactions that are important for biotechnology To teach enzymology and use of biochemical Internet information resources to advanced undergraduate and graduate students
Target Student Population:	Advanced undergraduate and graduate students
Prerequisite Knowledge or Skills:	An understanding of metabolism and biochemical pathways
Type of Material:	Database
Recommended Uses:	Could easily be used as a resource for an instructor to develop individual or group assignments. The site states that "The present database has been successfully used to teach enzymology and use of biochemical Internet information resources to advanced undergraduate and graduate students"
Technical Requirements:	Quicktime for animations

Rating:

Strengths:

Quality of Content: 5, 5 = 5

Features of Excellence

Currently there are over 100 pathways involving over 700 reactions related to
over 300 microorganisms.
Large set of contributors that makes the resources generated by a community of
active investigators with a review process that is designed to assure that
information presented on the site is accurate.
There are links to dynamic searches of the PubMed bibliographic database that
can assist in providing the user with the most recent findings related to the
topic of interest.
Information on Biocatalysis/Biodegradation that may be accessed from many directions e.g. chemical, microorganisms containing the process, pathways, organic functional groups, etc. The link organization is structured to allow a user to browse across the information in the database, e.g. starting with an organic functional can ultimately lead to a microorganism and visa versa.
The breath and extent of the site can be daunting at first. However, a "guided tour" and a set of Frequently Asked Questions (FAQ?s) is extremely helpful to the first time user as they provide definitions, interesting examples, and practice in navigating the database

Concerns:

The developers realize that there are limitations to how many pathways they can
include.
Because it is a volunteer effort, it is not clear how it will it keep up with the advances in this discipline. New input might be spotty

Rating:

Strengths:

Potential Effectiveness: 4, 4 = 4

Features of Excellence

There are several ways to access information about the relevant pathways and
components. This reinforces the relationships within metabolic systems.
This site represents a wealth of information that would otherwise be unavailable
The response time of the site is fast enough and it is fun to play with so that it would keep student interests and rapidly provide needed information for an investigation

Concerns:

The site assumes a high level of user knowledge. Inadequate background may prove
to be limiting factor for many students even at an advanced level
Really a professional database so that an instructor will have to write teaching modules

Rating:

Strengths:

Ease of Use: 4, 5 = 4.5

Features of Excellence

Fast response that generates information "on-the-fly", with links to appropriate resources outside of the database (PubMed, KEEG metabolic pathways, etc.)
There are detailed instructions for the user as well as a guided tour of the site.
User surveys are conducted every April, and the results are posted at the site. These serve to help the database developers remain focused on users needs. It is clear from comments in the "What is New" section that user input can lead to improvements
The "What's New" section allows one to easily access latest changes.

Concerns:

The complexity of metabolism are reflected in the complexity of the site and the opportunity to lose one's place.

Other Issues and Comments:

Overall: 4, 5 = 4.5

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