Pathway tools

SRI International Pathway Tools software supports creation, editing, querying, visualization, analysis, and publishing of Pathway/Genome Database (http // bioinformatics.ai.sri.com/ptools/)... 

Pathway Tools Omics Viewer EcoCyc—SRI International Paints data values from the user s high-throughput and other experiments onto the cellular overview diagram for an organism (http //biocyc.org/ expression.html)... 

Pathway Hole Filler can then be applied to predict likely genes to fill holes (missing steps) in predicted pathways. Thereafter, the Pathway Tools Navigator and Editor functions let users visualize, analyze, access, and update the database. Thus, by using PathoLogic and encyclopedias such as MetaCyc, an initial fast reconstruction can be developed automatically, and then, using the other units of Pathway Tools, a detailed manual update, curation, and verification step is possible. 

Pathway Tools conceptualizes the metabolic network in three layers. The first layer consists of the small-molecule substrates on which the metabolism operates. The second layer consists of the reactions that interconvert the small-molecule metabolites. The third layer is the metabolic pathways in which the components are the metabolic reactions of the second layer. Note that not all reactions in the second layer are included in pathways in the third layer because some metabolic reactions are not assigned to any metabolic pathway. 

In addition to the user-friendly graphical interfaces to PGDBs provided through the Web and desktop versions of Pathway Tools, we provide the following modes of access to PGDBs to facilitate the construction of programs that explore pathway data computationally. 

Pathway Tools can export PGDBs into several different file formats that are described at http //bioinformatics.ai.sri.com/ ptools/flatfile-format.html. These formats include column-delimited tables, SBML (see http //sbml.org/), BioPAX (see http //biopax.org/), Genbank, FASTA, and attribute-value. 

For those who want to query PGDB data through a relational database system, the attribute-value files exported by Pathway Tools can be loaded into SRFs BioWarehouse system (14). BioWarehouse is an Oracle or MySQL-based system for integration of multiple public bioinformatics databases. PGDB data can be queried through BioWarehouse alone or in combination with other bioinformatics databases such as UniProt, Genbank, NCBI Taxonomy, ENZYME, and KEGG. 

Queries using the pathway tools query language, BioVelo... 

Pathway Tools provides a powerful and easy-to-use query language for querying PGDBs, called BioVelo. See http //biocyc. org/query.html for details. 

Karp PD, Paley S Romero P. The Pathway Tools software. 

Paley SM, Karp PD. The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res. 2006 34 3771-3778. Green ML, Karp PD. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformat. 2004 5 76. 

Chapter 7—Pathways and Networks Minch and Vatcheva discuss the different types of pathway data, and they detail the various techniques of pathway analysis. They also include a useful summary of common public and commercial pathway tools and databases. 

Bernauer, S., D. Croft, P Gardina, E. Minch, M. de Rinaldis, and I. Vatcheva 2004. Case study Data management strategies in an integrated pathway tool. Appl Bioinformatics 3 63-75. 

Karp PD, Paley S, Romero P. The pathway tools software. Bioinformatics 2002 18(Suppl 1) S225-S232. 

V) Pathway Tool for analysis, expansion and visuali- http //www.ariadnegen-... 

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