skills.rest
jimmc414
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reactome-database

Query the Reactome REST API for pathway enrichment and gene-pathway mapping.

557|98|Updated Nov 7, 2025
Search Tags:#bioinformatics#pathway analysis#systems biology#reactome#gene enrichment#molecular interactions
One-click install
npx skills add https://github.com/jimmc414/Kosmos --skill reactome-database-jimmc414
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/jimmc414/Kosmos/tree/main/kosmos-claude-scientific-skills/scientific-skills/reactome-database/reactome-database
Command: npx skills add https://github.com/jimmc414/Kosmos --skill reactome-database-jimmc414

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, reactome2py, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill simplifies the complex task of analyzing biological pathways and understanding gene enrichment, making systems biology research more accessible.

Core Features & Use Cases

  • Pathway Enrichment Analysis: Identify statistically significant pathways from gene or protein lists.
  • Gene-Pathway Mapping: Map genes and proteins to their relevant biological pathways.
  • Data Retrieval: Query Reactome's extensive database for pathway information, molecular interactions, and disease mechanisms.
  • Use Case: Given a list of genes upregulated in a disease state, use this Skill to find the key biological pathways that are most affected, providing insights into disease mechanisms.

Quick Start

Use the reactome-database skill to perform pathway enrichment analysis on the gene list provided in 'my_genes.txt'.

Frequently Asked Questions about reactome-database

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

FAQPage Schema
How do I perform pathway enrichment analysis on a list of upregulated genes?▼

Pathway enrichment analysis identifies statistically significant biological pathways from gene or protein lists by querying the Reactome REST API. You submit your gene list to find key pathways affected in a disease state.

Can I map genes to molecular interactions and biological pathways using Reactome?▼

Yes, you can map genes and proteins to their relevant biological pathways and molecular interactions. Data retrieval queries Reactome's database for pathway information, interactions, and disease mechanisms.

Does this pathway analysis tool support species comparison and expression data analysis?▼

Yes, species comparison and expression data analysis are supported via direct API calls or a Python client. These features enable systems biology studies and overrepresentation analysis across different organisms.

What is the best way to query Reactome for systems biology studies programmatically?▼

The best way to query Reactome for systems biology studies is through the Reactome REST API or a Python client. This enables gene-pathway mapping, overrepresentation analysis, and molecular interactions data retrieval.

Do I need Python dependencies installed to use the Reactome database skill?▼

Yes, you need the requests and reactome2py Python dependencies installed. These packages facilitate direct API calls to the Reactome database for pathway analysis and gene enrichment tasks.

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