Reactome Database
If you're doing pathway enrichment or systems biology work, this gives you direct access to Reactome's 2,825+ curated human pathways through their REST API. You can run overrepresentation analysis on gene lists, analyze expression data, map proteins to pathways, and explore disease mechanisms. The API returns JSON with p-values and pathway mappings, plus tokens that stay valid for seven days so you can retrieve results later. It includes both the Content Service for querying pathway data and the Analysis Service for statistical enrichment. The reactome2py Python wrapper is available but hasn't been updated since 2021, so you might want to hit the REST endpoints directly for anything complex.
- skills.sh installs
- 252
- GitHub stars
- 33.2K
- last updated
- Aug 21, 2026
Install
$ npx -y skills add davila7/claude-code-templates --skill reactome-database --agent claude-codeInstalls into .claude/skills of the current project.
Files
Reactome Database
Overview
Reactome is a free, open-source, curated pathway database with 2,825+ human pathways. Query biological pathways, perform overrepresentation and expression analysis, map genes to pathways, explore molecular interactions via REST API and Python client for systems biology research.
When to Use This Skill
This skill should be used when:
- Performing pathway enrichment analysis on gene or protein lists
- Analyzing gene expression data to identify relevant biological pathways
- Querying specific pathway information, reactions, or molecular interactions
- Mapping genes or proteins to biological pathways and processes
- Exploring disease-related pathways and mechanisms
- Visualizing analysis results in the Reactome Pathway Browser
- Conducting comparative pathway analysis across species
Core Capabilities
Reactome provides two main API services and a Python client library:
1. Content Service - Data Retrieval
Query and retrieve biological pathway data, molecular interactions, and entity information.
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- Repository
- github.com/davila7/claude-code-templates
- Categories
- Backend & APIs, Databases
- First seen
- Jun 3, 2026
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