Author: Peter Karp

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.

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).

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 EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways.

We propose a network protocol whereby a database administrator can provide information about changes to the identifiers of objects in their database via Internet, to allow other databases to maintain referential integrity.

We present a methodology for predicting the metabolic pathways of an organism from its genomic sequence.