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Updated: Jun 18, 2026
08:01
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
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
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.
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.
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