Author: Peter Karp

I propose an Enzyme Genomics Initiative, the goal of which is to obtain at least one protein sequence for each enzyme that has previously been characterized biochemically.

A Pathway/Genome Database for Helicobacter pylori is available at URL BioCyc.org. The database integrates the full genome of H. pylori with its computationally predicted metabolic pathways.

Our PathoLogic software can generate a PGDB from an annotated genome of an organism, predicting the metabolic reactions and pathways corresponding to the enzymes present in the annotation.

In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Protégé-2000, to the maintenance and development of GO.

We seek to determine the accuracy of computational methods for predicting metabolic pathways in sequenced genomes, and to understand the contributions of both the prediction algorithms, and the reference pathway databases used by those algorithms, to the prediction accuracy.

The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB).

MetaCyc is a metabolic-pathway database that describes 445 pathways and 1115 enzymes occurring in 158 organisms.

We define the process of annotating a previously annotated genome sequence as ‘re-annotation’, and examine the strengths and weaknesses of current manual and automatic genome-wide re-annotation approaches.

We present an algorithm that solves two related problems in the analysis of metabolic networks stored within a pathway/genome database.

The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids.