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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
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PathBank 2.0-the pathway database for model organism metabolomics
David S Wishart1,2,3,4, Ray Kruger1, Aadhavya Sivakumaran1
1Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Nucleic Acids Research
|November 14, 2023
Summary
PathBank 2.0 offers a major upgrade for metabolomics researchers, significantly expanding pathway data and enhancing usability for drug metabolism studies. This update improves pathway visualization and analysis tools for better data interpretation.
Area of Science:
- Metabolomics
- Bioinformatics
- Computational Biology
Background:
- PathBank and SMPDB have served the metabolomics community since 2010.
- Databases evolve to meet community needs and technological advancements.
Purpose of the Study:
- To introduce PathBank 2.0, detailing significant upgrades and improvements.
- To enhance the utility and accessibility of pathway information for researchers.
Main Methods:
- Expansion of canonical and total pathway counts.
- Improvements in pathway diagram and description quality.
- Integration of drug metabolism and mechanism pathways.
Main Results:
- Canonical pathways increased from 1720 to 6951.
- Total pathways surged from 110,234 to 605,359.
- Enhanced pathway visualization, filtering, and analysis tools introduced.
Conclusions:
- PathBank 2.0 offers substantial improvements in data scope and features.
- Upgrades enhance ease of use and applications for metabolomics data interpretation.
- New tools support drug metabolism research and pathway enrichment analysis.
