Author: Peter Karp

The encyclopedia of Escherichia coli genes and metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of E.coli .

This article will describe some of the uses of these databases and then provide descriptions of the metabolic databases available.

Collaborative knowledge base (KB) authoring environments are critical for the construction of high-performance KBs. In this paper, we present an environment that satisfies many of these goals.

Group contribution methods are frequently used for estimating physical properties of compounds from their molecular structures. An algorithm for estimating Gibbs energies of formation through group contribution methods has been automated in an object-oriented framework.

We describe a novel approach for predicting the function of a protein from its amino-acid sequence.

Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification.

The Encyclopedia of E. coli Genes and Metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of E. coli.

The Encyclopedia of Genes and Metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of Escherichia coli.

The GKB Editor is a generic editor and browser of knowledge bases (KBs) and ontologies – generic in the sense that it is portable across several frame knowledge representation systems (FRSs).

This article provides an overview of the DB-interoperation problem, and offers several solutions. It discusses how links are used in molecular biology DBs, and describes the potential stumbling blocks when DB links are created and used.

We describe the design and implementation of visual presentations that closely mimic those found in the biology literature, and employ a frame knowledge representation system (FRS) called HyperTHEO to manage the EcoCyc knowledge base.