Author: Peter Karp

The article explores the notion of computing with function, and explains the importance of ontologies of function to bioinformatics.

Here we present a computational analysis of the global properties of that network, which consists of 744 reactions that are catalyzed by 607 enzymes.

Both databases are queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools.

This paper reports on an effort among the authors to evaluate alternative ontology-exchange languages, and to recommend one or more languages for use within the larger bioinformatics community.

The marriage of high-throughput nucleotide sequencing with computational methods for the analysis of nucleotide and protein sequences have ushered in a new era of molecular biology.

We present an architecture for scalable frame representation systems (FRSs). KBs must be supported for rapid construction by a collaborative effort of teams of knowledge engineers through reuse of existing knowledge and software components.

We describe pathway-based analyses of the genomes of a number of medically relevant microorganisms, and a novel software tool that provides visualization of gene expression data on a diagram showing the whole metabolic network of the microorganism.

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 .