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Updated: Jun 6, 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

Reactome: a database of reactions, pathways and biological processes.

David Croft¹, Gavin O'Kelly, Guanming Wu

¹European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Nucleic Acids Research

|November 12, 2010

Summary

Reactome offers an updated bioinformatics database with enhanced tools for analyzing human biological pathways and reactions. This resource now integrates molecular interaction data and supports pathway analysis across multiple species.

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Area of Science:

Bioinformatics
Systems Biology
Molecular Biology

Background:

Reactome is a collaborative, open-source bioinformatics database detailing human pathways and reactions.
Recent development of an improved website enhances pathway browsing and data analysis capabilities.

Purpose of the Study:

To present the updated Reactome website and its advanced tools for pathway analysis.
To expand pathway data accessibility and analysis for non-human species.

Main Methods:

Utilizing Systems Biology Graphical Notation (SBGN) for pathway visualization in the Pathway Browser.
Integrating PSIQUIC web services to overlay curated pathways with molecular interaction data from various databases.
Employing orthology-based inference using Ensembl Compara for pathway reconstruction in 20 non-human species.

Main Results:

The new Reactome website features an improved Pathway Browser with zooming, scrolling, and event highlighting.
Pathway and Expression Analysis tools facilitate ID mapping, pathway assignment, and overrepresentation analysis.
Inferred pathway sets for 20 additional species are available, along with a Species Comparison tool.

Conclusions:

The updated Reactome platform provides a comprehensive and user-friendly resource for biological pathway exploration and analysis.
Enhanced cross-species analysis capabilities facilitate comparative systems biology research.
Ongoing collaborations aim to expand manually curated datasets for additional species within the Reactome framework.