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reactome-database

Run Reactome pathway enrichment and identifier mapping for gene/protein lists.

2.7k|283|Updated May 13, 2026
Search Tags:#pathway analysis#identifier mapping#reactome#diagram export#gene set enrichment#token-based results#api cli
One-click install
npx skills add https://github.com/google-deepmind/science-skills --skill reactome-database-google-deepmind
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/google-deepmind/science-skills/tree/main/skills/reactome_database
Command: npx skills add https://github.com/google-deepmind/science-skills --skill reactome-database-google-deepmind

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

Reactome pathway enrichment and identifier mapping can be complex, stateful, and hard to reproduce across species and workflows; this Skill streamlines those API-driven steps into a consistent file-based process.

Core Features & Use Cases

  • Pathway enrichment and analysis: Submit identifier lists for overrepresentation and projection-based analyses and work with results using tokens.
  • Identifier mapping & cross-referencing: Map gene/protein identifiers across Reactome entities and resolve cross-references to other database identifiers.
  • Deep pathway inspection & outputs: Retrieve pathway hierarchy, reaction participants, download result datasets (JSON/CSV/PDF), and export pathway/reaction diagrams (PNG/SVG).

Quick Start

Use the reactome-database skill to run enrichment for a gene/protein list in Homo sapiens and write the full results to an output file for later drill-down.

Frequently Asked Questions about reactome-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run Reactome pathway enrichment analysis for a gene list?▼

Run Reactome pathway enrichment by submitting a gene or protein identifier list to the CLI, which uses the Reactome Analysis Service to perform overrepresentation and projection-based analyses and writes results to a file.

What is token-based result reuse in pathway analysis?▼

Token-based result reuse allows you to reference and retrieve prior Reactome enrichment analysis outputs using a token, enabling later drill-down and data export without resubmitting the original identifier list.

How do I map gene identifiers across different biological databases?▼

Map gene or protein identifiers across databases by using the identifier mapping and cross-reference features to resolve Reactome entities to other database identifiers via the Content Service.

Can I export Reactome pathway diagrams as PNG or SVG?▼

Yes, you can export Reactome pathway and reaction diagrams as PNG or SVG files, and download full result datasets in JSON, CSV, or PDF formats through the dedicated CLI.

How do I filter pathway enrichment results by FDR or p-value?▼

Filter pathway enrichment results by applying FDR or p-value thresholds during analysis, allowing you to narrow down significant pathways and focus on the most relevant biological reactions.

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