reactome-databaselisted

# 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/