Reactome Analysis & Content Service

Prerequisites

1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
2. User Notification: If .licenses/reactome_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://reactome.org/license and https://reactome.org/cite, then (2) create the file recording the notification text and timestamp.

Overview

Reactome is a free, open-source, curated pathway database. This skill wraps both the Analysis Service (https://reactome.org/AnalysisService/) and the Content Service (https://reactome.org/ContentService/) providing pathway enrichment analysis, identifier mapping, reaction details, pathway hierarchy navigation, diagram export, cross-reference mapping, and search.

When to Use This Skill

• Performing pathway enrichment (overrepresentation) analysis on gene/protein lists
• Retrieving analysis results using a token from previous enrichment
• Identifying which genes or proteins were not found in a pathway analysis
• Analyzing gene expression data against pathway annotations
• Mapping identifiers to Reactome entities across species
• Retrieving reaction participants (inputs, outputs, catalysts, regulators)
• Navigating pathway hierarchy and listing top-level pathways
• Finding which complexes or sets contain a protein
• Exporting pathway/reaction diagrams (PNG/SVG) with gene highlighting
• Cross-referencing identifiers across databases (UniProt, Ensembl, etc.)
• Searching the Reactome knowledgebase
• Downloading analysis reports (PDF, CSV, JSON)
• Comparing pathways across species

Common Species IDs

Reference list for common research organisms:

• Homo sapiens
  • ID: 9606
• Mus musculus (Mouse)
  • ID: 48892
• Rattus norvegicus (Rat)
  • ID: 48895

Common Pathway IDs