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Updated: Jan 5, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

PathBank: a comprehensive pathway database for model organisms.

David S Wishart^1,2, Carin Li¹, Ana Marcu¹

¹Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Nucleic Acids Research

|October 12, 2019

Summary

This summary is machine-generated.

PathBank is a comprehensive pathway database featuring over 110,000 machine-readable pathways across 10 model organisms. This resource supports pathway discovery in systems biology and offers downloadable data in multiple formats.

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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

Area of Science:

Systems Biology
Bioinformatics
Genomics

Background:

Biological pathways are fundamental to understanding cellular functions and disease mechanisms.
Existing pathway databases often lack comprehensive coverage or machine-readable formats.
The integration of multi-omics data necessitates robust pathway resources.

Purpose of the Study:

To introduce PathBank, a novel, extensive, and visually rich pathway database.
To support pathway elucidation and discovery in systems biology research.
To provide a pathway for every protein and a map for every metabolite.

Main Methods:

Curated and integrated pathway data from 10 model organisms.
Developed machine-readable pathway formats (BioPAX, SBML, PWML, SBGN, RXN).
Implemented web-based tools for visualization and community annotation (PathWhiz).

Main Results:

PathBank contains over 110,000 machine-readable pathways.
Pathways cover metabolic, signaling, disease, drug, and physiological processes.
Over 95% of PathBank pathways are unique and not found in other databases.

Conclusions:

PathBank serves as a valuable resource for systems biology, transcriptomics, proteomics, and metabolomics.
The database facilitates pathway discovery and elucidation through comprehensive and accessible data.
PathBank's extensive collection and machine-readable formats enhance biological research capabilities.