# Reactome Database

Query the Reactome database (Analysis and Content Services).

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Data and ML
- License: Apache-2.0
- Last updated: 2026-10-23
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add google-deepmind/science-skills --skill reactome-database -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill reactome-database -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill reactome-database -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill reactome-database -g -a gemini-cli -y`

## Description

Query the Reactome database (Analysis and Content Services). Use when the user asks about pathway analysis, gene list enrichment, retrieving results by token, finding unmapped or not-found identifiers, mapping identifiers, reaction participants (inputs, outputs), pathway hierarchy (including top-level pathways), diagram export, cross-reference mapping, or searching the knowledgebase.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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

The rest: https://github.com/google-deepmind/science-skills/blob/HEAD/skills/reactome_database/SKILL.md