Do I need an API key for this skill?

No, the Reactome Content and Analysis services are publicly accessible via REST API and do not require an API key for standard queries and analysis.

Can I use this skill for non-human species?

Yes, while Reactome focuses on human pathways, the skill supports species projection which allows you to map identifiers from other organisms to their human orthologs.

Reactome is a free, open-source, curated database of human biological pathways and reactions used for systems biology research and data visualization.

What gene identifier types are supported?

The skill supports a wide range of identifiers including UniProt accessions, Gene symbols, Ensembl IDs, EntrezGene IDs, and ChEBI IDs for small molecules.

How do I visualize my analysis results?

The skill generates analysis tokens that can be used to construct URLs for the Reactome Pathway Browser, allowing you to view your results in an interactive web interface.

Reactome Pathway Database & Analysis

Name: Reactome Pathway Database & Analysis
Author: jimmc414

byjimmc414

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324

Data Science & ML

Accesses the Reactome database to perform biological pathway analysis, gene mapping, and enrichment studies for systems biology.

About

The Reactome Database skill integrates comprehensive biological pathway data into Claude Code, enabling researchers and bioinformaticians to perform advanced systems biology tasks directly within their workflow. It provides access to over 2,800 human pathways, allowing users to conduct overrepresentation analysis on gene lists, analyze expression data, map molecular interactions, and visualize results through the Reactome Pathway Browser. By bridging the gap between raw genomic data and functional biological insights, this skill facilitates autonomous discovery and detailed mechanistic studies of diseases and cellular processes.

Key Features

324 GitHub stars
Direct retrieval of molecular interactions and entity hierarchies
Automated pathway enrichment and overrepresentation analysis
Gene expression dataset analysis with quantitative values
Cross-species comparative pathway analysis and projections
Integration with the Reactome Pathway Browser for visualization

Use Cases

Identifying biological mechanisms underlying differentially expressed genes in a study
Exploring disease-related pathways to understand molecular drivers of pathology
Mapping high-throughput proteomics data to curated human pathways and reactions

About

Key Features

324 GitHub stars
Direct retrieval of molecular interactions and entity hierarchies
Automated pathway enrichment and overrepresentation analysis
Gene expression dataset analysis with quantitative values
Cross-species comparative pathway analysis and projections
Integration with the Reactome Pathway Browser for visualization

Use Cases

Identifying biological mechanisms underlying differentially expressed genes in a study
Exploring disease-related pathways to understand molecular drivers of pathology
Mapping high-throughput proteomics data to curated human pathways and reactions