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This paper provides an overview of the four main components of the Pathway Tools: The PathoLogic component supports creation of new Pathway/Genome Database from the annotated genome of an organism

The Pathway Tools software.

ISMB, (2002): 225-232

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摘要

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...更多

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简介
  • The Pathway Tools is a software environment for creating a type of model-organism database (MOD) called a

    Pathway/Genome Database (PGDB).
  • The Pathway Tools is a software environment for creating a type of model-organism database (MOD) called a.
  • A PGDB integrates information about the genes, proteins, metabolic network, and genetic network of an organism.
  • In 1997 the authors began to generalize the software so that it could be applied to manage genome data from other organisms besides E.
  • Coli, and so that it could simultaneously manage data from multiple organisms to facilitate comparative genomics studies
  • In 1997 the authors began to generalize the software so that it could be applied to manage genome data from other organisms besides E. coli, and so that it could simultaneously manage data from multiple organisms to facilitate comparative genomics studies
重点内容
  • The Pathway Tools is a software environment for creating a type of model-organism database (MOD) called a

    Pathway/Genome Database (PGDB)
  • 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 Tools ontology defines the schema of PGDBs
  • PGDB: it provides a graphical environment that allows users to visualize the contents of a PGDB and to interactively update a PGDB; and it provides a sophisticated ontology and database API that allow programs to perform
  • The software has been used for global studies of the E. coli metabolic network (Ouzounis and Karp, 2000) and genetic network (Karp, 2001)
  • SRI to construct 13 different PGDBs; construction of another 8–10 databases is under way at SRI and by other scientists
结果
  • The Pathway Tools is a reusable, productionquality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB).
  • 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.
  • 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
结论
  • The Pathway Tools software supports creation of new

    PGDBs using its PathoLogic component.
  • The Pathway Tools software supports creation of new.
  • The Pathway/Genome Editors support interactive refinement of PGDBs by MOD curators.
  • Navigator provides Web publishing of PGDBs, and supports many forms of interactive queries, visualization, and analysis.
  • The Pathway Tools have been used at.
  • SRI to construct 13 different PGDBs; construction of another 8–10 databases is under way at SRI and by other scientists
基金
  • This work was supported by grant 1-R01-RR07861-01 from the National Center for Research Resources, by grant DE-FG03-01ER6321 from the Department of Energy, and by DARPA contract N66001-01-C-8011
研究对象与分析
microbial genomes: 11
PathoLogic is configured to err on the side of more liberal pathway predictions on the assumption that it is better to bring questionable pathway predictions to the attention of the scientist user for further study than to omit those pathways from consideration. SRI has applied PathoLogic to 11 microbial genomes. The resulting PGDBs are available through the SRI web site at URL http://biocyc.org

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