Review of KEGG Encyclopedia

Title: Kyoto Encyclopedia of Genes and Genomes

Date Reviewed: 5/30/01

Description: KEGG is an effort to categorize biological processes (from separate organisms) in terms of information pathways (e.g. metabolic pathways, regulatory pathways, and molecular assemblies)

), with links to the genetic/genomic information about members of the pathways. Kegg also "maintains gene catalogs for all the organisms that have been sequenced and links each gene product to a component on the pathway". Kegg also "organizes a database of all chemical compounds in living cells and links each compound to a pathway component." A future goal is to be able to use KEGG for functional reconstruction processes.

Strengths: Attempts to link biological molecules into the framework of a pathway. Has links from a particular pathway in a particular organism to all the relevant genetic/genomic information and links to things like OMIM etc.

Weaknesses: I attempted to find the pathways p53 are a part of (since there are cell cycles pathways they have compiled) and basically was unable to do it. You are supposed to search for the gene name first and be able to put it into the path search page, but essentially it’s not fully integrated yet. For instance I can go to regulatory pathways:cell cycle:human and click on p53 (and get all the further links to this pathway component), but I can’t search human pathways for p53 and get the cell cycle.

Comprehensiveness:

Timeliness: Fine/good

Ease of Use: Not very (see above) for searching there pathways for a known molecule

Responsiveness: fine/good

Overall Evaluation: 2

Reviewer:Susan Schonhoff

Email:susan.schonhoff@tufts.edu