Author: Peter Karp

Genome-context methods have proved useful in providing clues about functional annotations for many proteins. They detect many biological types of functional associations, and do not identify which type of functional association they have found. We have developed two new genome-context-based algorithms.

Here we present a follow-up literature-based survey involving a statistically significant sample of such “orphan” activities.

The Pathway Tools software allows a group of scientists to create, update, and publish on the Web an evolving knowledge resource describing the genome and biochemical networks of the organism.

Pathway Tools supports interrogation and exploration of cellular biochemical networks through the overview diagram and a software component called the Omics Viewer.

MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments.

Using the completed V.cholerae genome sequence and PathoLogic software, we created VchoCyc, a pathway-genome database that predicted 171 likely metabolic pathways in the bacterium.

We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers.

Different biological notions of pathways are used in different pathway databases. Those pathway ontologies significantly impact pathway computations.

In conjunction with the Pathway Tools software, MetaCyc can be used to computationally predict the metabolic pathway complement of an annotated genome.

The BioWarehouse is an open source data warehousing environment focused on supporting bioinformatics databases (DBs). BioWarehouse integrates public source DBs such as Swiss-Prot and GenBank into a unified normalized schema operating under a single DB management system.