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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.

Peter D Karp1, Suzanne M Paley, Markus Krummenacker

  • 1Artificial Intelligence Center, SRI International, 333 Ravenswood Ave, AE206, Menlo Park, CA 94025, USA. pkarp@ai.sri.com

Briefings in Bioinformatics
|December 4, 2009
PubMed
Summary

Pathway Tools software aids in creating Pathway/Genome Databases (PGDBs) for model organisms. It offers computational inferences, data integration, and comparative analyses for systems biology research.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Pathway/Genome Databases (PGDBs) integrate genomic and functional data for organisms.
  • Model-organism databases are crucial for understanding biological systems.

Purpose of the Study:

  • To provide an overview of the capabilities of the Pathway Tools software environment.
  • To highlight its utility in creating, managing, and analyzing PGDBs.

Main Methods:

  • The software facilitates the creation and interactive editing of PGDBs.
  • It performs computational inferences like metabolic pathway and operon prediction.
  • Supports comparative and systems biology analyses, including network reachability and metabolite tracing.

Main Results:

  • Over 800 PGDBs have been developed worldwide using Pathway Tools.
  • The software enables web publishing and peer-to-peer sharing of PGDBs via the PGDB Registry.
  • It provides extensive query and visualization tools for PGDB data.

Conclusions:

  • Pathway Tools is a comprehensive environment for building and analyzing PGDBs.
  • It supports collaborative research through data sharing and advanced analytical features.
  • Facilitates the integration of diverse biological data for systems-level understanding.