Bioinformatics publications
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The MetaCyc Database
MetaCyc is a metabolic-pathway database that describes 445 pathways and 1115 enzymes occurring in 158 organisms.
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The genome of the natural genetic engineer Agrobacterium tumefaciens C58
The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids.
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Nutrient-related Analysis of Pathway/Genome Databases
We present an algorithm that solves two related problems in the analysis of metabolic networks stored within a pathway/genome database.
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XOL: An XML-Based Ontology Exchange Language
This document describes a language called XOL, is designed to provide a format for exchanging ontology definitions among a set of interested parties.
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Global Properties of the Metabolic Map of Escherichia coli
Here we present a computational analysis of the global properties of that network, which consists of 744 reactions that are catalyzed by 607 enzymes.
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An Ontology for Biological Function Based on Molecular Interactions
The article explores the notion of computing with function, and explains the importance of ontologies of function to bioinformatics.
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The EcoCyc and MetaCyc Databases
Both databases are queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools.
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An Evaluation of Ontology Exchange Languages for Bioinformatics
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.
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EcoCyc: Electronic Encyclopedia of E. coli Genes and Metabolism
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What we do not know about sequence analysis and sequence databases
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.
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Integrated Pathway/Genome Databases and Their Role in Drug Discovery
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…
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A Collaborative Environment for Authoring Large Knowledge Bases
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…