title: The Pathway Tools software.
abstract: BACKGROUND
  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.affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA, 94025, USA. pkarp@ai.sri.com
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
authors.forename: Suzanne
authors.initials: S
authors.lastname: Paley
authors.forename: Pedro
authors.initials: P
authors.lastname: Romero
mesh_terms: D000043:Abstracting and Indexing / Q000379:methods; D000818:Animals; D003628:Database Management Systems; D030541:Databases, Genetic; D005786:Gene Expression Regulation / Q000502:physiology*; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D008954:Models, Biological; D020543:Proteome / Q000235:genetics* / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology; D012984:Software; D014584:User-Computer Interface
chemical_list: D020543:Proteome