What is the source of the pathway data?

Data is sourced from Reactome, a free, open-source, curated, and peer-reviewed pathway database used globally for biological research.

Can I perform expression analysis with this skill?

Yes, you can submit TSV-formatted expression data with numeric values to identify pathways relevant to your specific experimental conditions.

What types of identifiers does this skill support?

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

Does this work for non-human species?

Yes, the skill includes support for species projection, allowing you to map identifiers from other organisms to equivalent human pathways.

How long are analysis tokens valid for?

Analysis tokens generated via the Reactome Analysis Service are valid for 7 days, allowing you to retrieve results without re-submitting data.

Reactome Database Integration

Name: Reactome Database Integration
Author: Microck

byMicrock

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Data Science & ML

Integrates Reactome's open-source curated pathway database for biological pathway analysis, gene mapping, and systems biology research.

About

The Reactome Database skill provides a robust interface for researchers and bioinformaticians to interact with the Reactome REST API directly through Claude. It facilitates comprehensive systems biology studies by enabling automated pathway enrichment analysis, molecular interaction queries, and the mapping of gene or protein lists to specific biological processes. With support for both the Reactome Content Service for data retrieval and the Analysis Service for computational workflows, this skill streamlines the exploration of over 2,800 human pathways and helps visualize complex experimental results in the Reactome Pathway Browser.

Key Features

Generate visualization links for the Reactome Pathway Browser
Analyze quantitative expression data for pathway enrichment
81 GitHub stars
Query detailed molecular interactions and reaction hierarchies
Perform overrepresentation analysis on gene and protein lists
Map various identifiers including UniProt, Ensembl, and Gene symbols

Use Cases

Analyzing transcriptomic or proteomic datasets to discover disease-related mechanisms
Retrieving curated molecular interaction data for systems biology modeling
Identifying statistically significant biological pathways from experimental gene lists

About

Key Features

Generate visualization links for the Reactome Pathway Browser
Analyze quantitative expression data for pathway enrichment
81 GitHub stars
Query detailed molecular interactions and reaction hierarchies
Perform overrepresentation analysis on gene and protein lists
Map various identifiers including UniProt, Ensembl, and Gene symbols

Use Cases

Analyzing transcriptomic or proteomic datasets to discover disease-related mechanisms
Retrieving curated molecular interaction data for systems biology modeling
Identifying statistically significant biological pathways from experimental gene lists