Author: Suzanne Paley
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Querying and Computing with BioCyc Databases
We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases.
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EcoCyc: a comprehensive database resource for Escherichia coli
The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli.
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An Evidence Ontology for use in Pathway/Genome Databases
This paper presents an ontology for encoding the type of support and the degree of support for DB assertions, and for encoding the literature source in which that support is reported.
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MetaCyc: a multiorganism database of metabolic pathways and enzymes
In the past 2 years the data content and the Pathway Tools software used to query, visualize and edit MetaCyc have been expanded significantly. These enhancements are described in this paper.
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HpyCyc: Helicobacter pylori Pathway/Genome Database
A Pathway/Genome Database for Helicobacter pylori is available at URL BioCyc.org. The database integrates the full genome of H. pylori with its computationally predicted metabolic pathways.
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Evaluation of computational metabolic-pathway predictions for Helicobacter pylori
We seek to determine the accuracy of computational methods for predicting metabolic pathways in sequenced genomes, and to understand the contributions of both the prediction algorithms, and the reference pathway databases used by those algorithms, to the prediction accuracy.
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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 Pathway Tools Software
The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB).
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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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EcoCyc: Electronic Encyclopedia of E. coli Genes and Metabolism
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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 knowledge and software components.
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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 the whole metabolic network of the microorganism.