Literature DB >> 11557880

Pathway databases: a case study in computational symbolic theories.

P D Karp1.   

Abstract

A pathway database (DB) is a DB that describes biochemical pathways, reactions, and enzymes. The EcoCyc pathway DB (see http://ecocyc.org) describes the metabolic, transport, and genetic-regulatory networks of Escherichia coli. EcoCyc is an example of a computational symbolic theory, which is a DB that structures a scientific theory within a formal ontology so that it is available for computational analysis. It is argued that by encoding scientific theories in symbolic form, we open new realms of analysis and understanding for theories that would otherwise be too large and complex for scientists to reason with effectively.

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Year:  2001        PMID: 11557880     DOI: 10.1126/science.1064621

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  51 in total

1.  The EcoCyc Database.

Authors:  Peter D Karp; Monica Riley; Milton Saier; Ian T Paulsen; Julio Collado-Vides; Suzanne M Paley; Alida Pellegrini-Toole; César Bonavides; Socorro Gama-Castro
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

2.  The phylogenetic extent of metabolic enzymes and pathways.

Authors:  José Manuel Peregrin-Alvarez; Sophia Tsoka; Christos A Ouzounis
Journal:  Genome Res       Date:  2003-03       Impact factor: 9.043

3.  PROTEOME-3D: an interactive bioinformatics tool for large-scale data exploration and knowledge discovery.

Authors:  Deborah H Lundgren; Jimmy Eng; Michael E Wright; David K Han
Journal:  Mol Cell Proteomics       Date:  2003-09-07       Impact factor: 5.911

4.  Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors:  Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

5.  In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism.

Authors:  Masanori Arita
Journal:  Genome Res       Date:  2003-10-14       Impact factor: 9.043

6.  Information Visualization Techniques in Bioinformatics during the Postgenomic Era.

Authors:  Ying Tao; Yang Liu; Carol Friedman; Yves A Lussier
Journal:  Drug Discov Today Biosilico       Date:  2004-11

7.  Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.

Authors:  Peter D Karp; Mario Latendresse; Suzanne M Paley; Markus Krummenacker; Quang D Ong; Richard Billington; Anamika Kothari; Daniel Weaver; Thomas Lee; Pallavi Subhraveti; Aaron Spaulding; Carol Fulcher; Ingrid M Keseler; Ron Caspi
Journal:  Brief Bioinform       Date:  2015-10-10       Impact factor: 11.622

8.  A proposal for augmenting biological model construction with a semi-intelligent computational modeling assistant.

Authors:  Scott Christley; Gary An
Journal:  Comput Math Organ Theory       Date:  2012-12       Impact factor: 2.023

9.  Visualizing information across multidimensional post-genomic structured and textual databases.

Authors:  Ying Tao; Carol Friedman; Yves A Lussier
Journal:  Bioinformatics       Date:  2004-12-14       Impact factor: 6.937

10.  Molecular models of protein targets from Mycobacterium tuberculosis.

Authors:  Nelson José Freitas da Silveira; Hugo Brandão Uchôa; José Henrique Pereira; Fernanda Canduri; Luiz Augusto Basso; Mário Sérgio Palma; Diógenes Santiago Santos; Walter Filgueira de Azevedo
Journal:  J Mol Model       Date:  2005-03-10       Impact factor: 1.810

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