skills.rest
Sologa
SologaCOMMUNITY
Explore all skills by this author →
GitHub

reactome-database

Query Reactome REST API and reactome2py for pathway enrichment and gene mapping.

1|Updated Jan 14, 2026
Search Tags:#bioinformatics#pathway analysis#systems biology#reactome#gene enrichment#molecular interactions
One-click install
npx skills add https://github.com/Sologa/codex-pipeline --skill reactome-database-sologa
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/Sologa/codex-pipeline/tree/main/.codex/skills/reactome-database
Command: npx skills add https://github.com/Sologa/codex-pipeline --skill reactome-database-sologa

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides access to the Reactome database, enabling users to query biological pathways, perform enrichment analysis, and map genes to pathways for systems biology research.

Core Features & Use Cases

  • Pathway Enrichment Analysis: Identify significant biological pathways from gene lists.
  • Gene-Pathway Mapping: Find pathways associated with specific genes or proteins.
  • Data Retrieval: Access detailed information about pathways, reactions, and molecular interactions.
  • Use Case: A researcher has a list of differentially expressed genes from an RNA-seq experiment and wants to understand the underlying biological processes. They can use this Skill to perform overrepresentation analysis and identify significantly enriched pathways.

Quick Start

Use the reactome-database skill to perform overrepresentation 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 differentially expressed genes?▼

Pathway enrichment analysis identifies significant biological pathways from gene lists by processing your data against curated human pathways. You can use this Skill to perform overrepresentation analysis and map genes to pathways for systems biology research.

Can I retrieve molecular interaction data and pathway details from the Reactome database?▼

Molecular interaction data retrieval from the Reactome database queries the REST API using the reactome2py Python package. This provides access to detailed information about biological pathways, reactions, and molecular interactions for systems biology studies.

What is gene-pathway mapping and how does it work with Reactome?▼

Gene-pathway mapping finds biological pathways associated with specific genes or proteins by querying the Reactome database. It processes your gene lists against curated human pathways to identify underlying biological processes.

How do I map RNA-seq expression data to biological pathways?▼

RNA-seq expression data is mapped to biological pathways by processing gene lists against curated human pathways in Reactome. This Skill performs overrepresentation analysis to identify significantly enriched pathways from your differentially expressed genes.

Does reactome2py support overrepresentation analysis for systems biology research?▼

The reactome2py package supports overrepresentation analysis for systems biology research by querying the Reactome REST API. It enables pathway enrichment analysis and gene-pathway mapping using curated human pathways.

What's the best way to identify significant biological pathways from a gene list?▼

Identifying significant biological pathways from a gene list is best achieved through pathway enrichment analysis. This Skill queries the Reactome database to perform overrepresentation analysis and map genes to curated human pathways.

Related Skills

Explore More Education & Research Skills→
OwnLabAIOwnLabAI
21

arboreto

Infer gene regulatory networks from RNA-seq data using GRNBoost2 or GENIE3.

Official
Advanced
hxk622hxk622
8

reactome-database

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

Community
Intermediate
omicverseomicverse
32

bulk-rna-seq-differential-expression-with-omicverse

Analyze bulk RNA-seq count matrices for differential expression and pathway enrichment.

Official
Advanced
Yezez9Yezez9

reactome-database

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

Community
Intermediate