reactome-database

1# Reactome Analysis & Content Service
2 
3## Prerequisites
4 
51.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
6    `uv` is installed and on PATH.
72.  **User Notification**: If .licenses/reactome_database_LICENSE.txt does not
8    already exist in the workspace root directory then (1) prominently notify
9    the user to check the terms at https://reactome.org/license and
10    https://reactome.org/cite, then (2) create the file recording the
11    notification text and timestamp.
12 
13## Overview
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15Reactome is a free, open-source, curated pathway database. This skill wraps both
16the **Analysis Service** (`https://reactome.org/AnalysisService/`) and the
17**Content Service** (`https://reactome.org/ContentService/`) providing pathway
18enrichment analysis, identifier mapping, reaction details, pathway hierarchy
19navigation, diagram export, cross-reference mapping, and search.
20 
21## When to Use This Skill
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23-   Performing pathway enrichment (overrepresentation) analysis on gene/protein
24    lists
25-   Retrieving analysis results using a token from previous enrichment
26-   Identifying which genes or proteins were not found in a pathway analysis
27-   Analyzing gene expression data against pathway annotations
28-   Mapping identifiers to Reactome entities across species
29-   Retrieving reaction participants (inputs, outputs, catalysts, regulators)
30-   Navigating pathway hierarchy and listing top-level pathways
31-   Finding which complexes or sets contain a protein
32…