Peter D Karp1, Suzanne Paley, Pedro Romero. 1. Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA, 94025, USA. pkarp@ai.sri.com
Abstract
MOTIVATION: Bioinformatics requires reusable software tools for creating model-organism databases (MODs). RESULTS: The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc (see http://ecocyc.org) integrates our evolving understanding of the genes, proteins, metabolic network, and genetic network of an organism. This paper provides an overview of the four main components of the Pathway Tools: The PathoLogic component supports creation of new PGDBs from the annotated genome of an organism. The Pathway/Genome Navigator provides query, visualization, and Web-publishing services for PGDBs. The Pathway/Genome Editors support interactive updating of PGDBs. The Pathway Tools ontology defines the schema of PGDBs. The Pathway Tools makes use of the Ocelot object database system for data management services for PGDBs. The Pathway Tools has been used to build PGDBs for 13 organisms within SRI and by external users.
MOTIVATION: Bioinformatics requires reusable software tools for creating model-organism databases (MODs). RESULTS: The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc (see http://ecocyc.org) integrates our evolving understanding of the genes, proteins, metabolic network, and genetic network of an organism. This paper provides an overview of the four main components of the Pathway Tools: The PathoLogic component supports creation of new PGDBs from the annotated genome of an organism. The Pathway/Genome Navigator provides query, visualization, and Web-publishing services for PGDBs. The Pathway/Genome Editors support interactive updating of PGDBs. The Pathway Tools ontology defines the schema of PGDBs. The Pathway Tools makes use of the Ocelot object database system for data management services for PGDBs. The Pathway Tools has been used to build PGDBs for 13 organisms within SRI and by external users.
Authors: Cynthia J Krieger; Peifen Zhang; Lukas A Mueller; Alfred Wang; Suzanne Paley; Martha Arnaud; John Pick; Seung Y Rhee; Peter D Karp Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971
Authors: Wilbert B Copeland; Bryan A Bartley; Deepak Chandran; Michal Galdzicki; Kyung H Kim; Sean C Sleight; Costas D Maranas; Herbert M Sauro Journal: Metab Eng Date: 2012-05 Impact factor: 9.783
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
Authors: Karen R Christie; Shuai Weng; Rama Balakrishnan; Maria C Costanzo; Kara Dolinski; Selina S Dwight; Stacia R Engel; Becket Feierbach; Dianna G Fisk; Jodi E Hirschman; Eurie L Hong; Laurie Issel-Tarver; Robert Nash; Anand Sethuraman; Barry Starr; Chandra L Theesfeld; Rey Andrada; Gail Binkley; Qing Dong; Christopher Lane; Mark Schroeder; David Botstein; J Michael Cherry Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971
Authors: Andrew M Bailey; Al Ivens; Rob Kingsley; Jennifer L Cottell; John Wain; Laura J V Piddock Journal: J Bacteriol Date: 2010-01-15 Impact factor: 3.490