reactome-database

Este extracto es una copia guardada durante la revisión. La fuente externa contiene la versión completa y actual.

---
name: reactome-database
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.
---

# 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

Reference list for commonly used Reactome pathway stable IDs:

-   Cell Cycle
    -   Stable ID: R-HSA-1640170
    -   Notes: Top-level pathway (broad)
-   Cell Cycle, Mitotic
    -   Stable ID: R-HSA-69278
    -   Notes: Specific sub-pathway — use this for diagrams and drill-downs
-   Immune System
    -   Stable ID: R-HSA-168256
    -   Notes: Top-level pathway
-   Signal Transduction
    -   Stable ID: R-HSA-162582
    -   Notes: Top-level pathway
-   Gene Expression
    -   Stable ID: R-HSA-74160
    -   Notes: Top-level pathway
-   Programmed Cell Death
    -   Stable ID: R-HSA-5357801
    -   Notes: Top-level pathway

> **Important**: When the user asks for a "Cell Cycle" diagram or analysis,
> prefer the specific **Cell Cycle, Mitotic** pathway (`R-HSA-69278`) unless the
> user explicitly requests the top-level overview. The examples throughout this
> document use `R-HSA-69278`.

## Core Rules

1.  **Always use `--output`**: Every subcommand requires `--output <file>` to
    write results to a file. Never rely on stdout for large results.
2.  **Default species is Homo sapiens**: Use `--species` to override.
3.  **Tokens expire after 7 days**: Store tokens from analysis results to
    retrieve them later without re-submitting data.
4.  **Use `--fdr` and `--pvalue` to filter**: Enrichment results can be
    overwhelming. Filter with `--fdr 0.05` or `--pvalue 0.01` to focus on
    statistically significant pathways.
5.  **Identifier formats**: Reactome auto-detects identifiers including gene
    symbols (TP53), UniProt (P04637), Ensembl (ENSG0000014