How do I visualize the results of my pathway analysis?

The skill can generate analysis tokens which you can append to Reactome Pathway Browser URLs to visualize your results in a web interface.

Which identifiers are supported for gene mapping?

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

What is the Reactome Database skill used for?

It is used to query curated biological pathway data, perform statistical enrichment analysis on gene lists, and map molecular interactions for bioinformatics research.

Does this skill require a Reactome API key?

No, the Reactome REST API is free and open-source, allowing you to perform queries and analysis without a specific API key.

Can I use this skill for species other than humans?

Yes, Reactome supports species comparison and the projection of non-human data onto human pathways for comparative analysis.

Reactome Database Bio-Analysis

Name: Reactome Database Bio-Analysis
Author: Yezez9

byYezez9

0•

Data Science & ML

Queries the Reactome REST API to perform biological pathway analysis, gene enrichment, and molecular interaction mapping for systems biology research.

The Reactome Database skill integrates comprehensive biological pathway data into AI-assisted research workflows. It enables users to perform sophisticated overrepresentation analysis on gene or protein lists, analyze quantitative expression datasets, and map specific entities to curated human pathways. By leveraging Reactome's Content and Analysis services, this skill facilitates deep exploration of molecular reactions, disease mechanisms, and comparative species analysis. It is an essential tool for bioinformaticians and systems biologists looking to automate data retrieval and gain functional insights from complex omics data.

Key Features

01Comprehensive retrieval of pathway hierarchies, reactions, and participating entities

02Direct generation of visualization links for the Reactome Pathway Browser

03Cross-species pathway comparison and projection to human models

04Statistical overrepresentation analysis for gene and protein identifiers

05Quantitative expression data analysis to identify significant biological pathways

060 GitHub stars

Use Cases

01Mapping lists of proteins or small molecules to their corresponding molecular reactions

02Automating the retrieval of database versioning and metadata for reproducible research

03Identifying enriched biological pathways from differential gene expression results

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent reactome-database

For use in Claude.ai and ChatGPT

Key Features

01Comprehensive retrieval of pathway hierarchies, reactions, and participating entities

02Direct generation of visualization links for the Reactome Pathway Browser

03Cross-species pathway comparison and projection to human models

04Statistical overrepresentation analysis for gene and protein identifiers

05Quantitative expression data analysis to identify significant biological pathways

060 GitHub stars

Use Cases

01Mapping lists of proteins or small molecules to their corresponding molecular reactions

02Automating the retrieval of database versioning and metadata for reproducible research

03Identifying enriched biological pathways from differential gene expression results