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reactome-database

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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.

skills/reactome_database/SKILL.md

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Network or broad shell
Last checked
Nov 9, 2026

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3,438
Repository last updated
Oct 23, 2026
License
Apache-2.0

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# 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
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