Can I use this for gene expression analysis?

Yes, the skill supports submitting expression datasets in TSV format to identify relevant pathways based on quantitative values.

What identifiers are supported for mapping?

The system automatically detects UniProt accessions, Gene symbols, Ensembl IDs, EntrezGene IDs, and ChEBI IDs for small molecules.

What is the Reactome Database skill?

It is a specialized capability for Claude to query biological pathway data and perform enrichment analysis using the Reactome REST API and Python tools.

Does it support non-human species?

While Reactome is human-centric, the skill includes capabilities for species projection and comparative pathway analysis across various organisms.

How long do analysis tokens remain valid?

Analysis tokens generated by the Reactome Analysis Service are valid for 7 days, allowing you to retrieve results across different sessions.

Reactome Biological Pathways & Analysis

Name: Reactome Biological Pathways & Analysis
Author: ricable

byricable

•

Data Science & ML

Queries the Reactome database to perform biological pathway analysis, gene-pathway mapping, and expression enrichment for systems biology research.

The Reactome Database skill empowers researchers and developers to interact with the world's leading open-source biological pathway database directly through Claude. It provides seamless access to over 2,800 human pathways, enabling tasks such as overrepresentation analysis for gene lists, expression data mapping, and deep exploration of molecular interactions. Whether you are identifying statistically significant pathways from experimental data or visualizing disease mechanisms in the Reactome Pathway Browser, this skill simplifies complex systems biology workflows by integrating REST API calls and Python-based analysis scripts into your development environment.

Key Features

011 GitHub stars

02Generate visualization links for the Reactome Pathway Browser

03Map gene expression data to identified biological pathways

04Perform overrepresentation analysis on gene and protein lists

05Explore curated disease-related mechanisms and pathways

06Retrieve detailed molecular interaction and reaction data

Use Cases

01Identifying enriched biological processes in transcriptomic datasets

02Comparing pathway data across human and non-human species

03Mapping unknown protein lists to specific cellular reactions

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add ricable/ultimate-ai-agent reactome-database

For use in Claude.ai and ChatGPT

Download Skill