- Web report
- Open Access
Digital biochemical pathways database
- Todd Richmond
© BioMed Central Ltd 2000
- Received: 2 August 2000
- Published: 18 September 2000
The ExPASy biochemical pathways database provides online access to the biochemical pathways index of Boehringer Mannheim.
- Enzyme Commission
- Pathway Database
- Online Access
- Enzyme Database
- Matching Entry
The ExPASy biochemical pathways database provides online access to the biochemical pathways index of Boehringer Mannheim. Most researchers in the life sciences are probably familiar with Boehringer's wallcharts of metabolic pathways - huge posters of complex, interconnecting metabolic processes. While these are fun to look at, it is often difficult to find exactly what you are looking for. The biochemical pathways database allows you quickly to determine the location of any metabolite or enzyme in the index.
Last updated 12 February 1999.
The website provides a very simple and easy-to-use launch pad for metabolic pathway information. With the increasing use of DNA microarrays and proteomics, researchers are faced with the need quickly to locate information about enzymes that they may never have heard of before.
Although the enzyme information is excellent, the information about the various metabolites is poor. For example, a search for glucose-6-phosphate brings up both glucose-6-phosphate dehydrogenase and glucose-6-phosphate isomerase, but nothing about the sugar itself. Using one of the enzymes above to get to the chart will give the structure of glucose-6-phosphate, but no other information is available.
There are several things that would greatly improve the utility of this database. First, some way to highlight on the chart picture the enzyme or metabolite that you searched for would be useful. As it is, you are presented with a scanned image of the chart, and have to hunt for the object of your search. Second, clicking anywhere on the graphic acts as a link and launches a new page. If you do not click on a blue-colored enzyme name, however, the following message appears: 'The part of the map you selected does not correspond to an enzyme. Please try again, clicking on any word of the map printed in blue.' It would be better to have only the enzyme names hot-linked to another page. Finally, the use of scanned pieces of the wall chart to show the data is limiting. As a database system, it would be nice if the diagrams were generated on-the-fly, using modern vector graphics. This would produce higher-quality images, possibly suitable for presentation, with a faster response time.
There are a number of enzyme and pathway databases, many of which can be reached from the individual enzyme listings in the biochemical pathways database. They include: WIT - What is there?, The Enzymology Database (EMP), BRENDA, the enzyme database, and the KEGG metabolic pathways database.