mcp-genelab by sbl-sdsc - MCP Server

MCP GeneLab Server

A Model Context Protocol (MCP) server that converts natural language queries into Cypher queries and executes them against the configured Neo4j endpoints. Customized tools provide seamless access to the NASA GeneLab Knowledge Graph, enabling AI-assisted analysis of spaceflight experiments and their biological effects. This server allows researchers to query differential gene expression and DNA methylation data from NASA's space biology experiments through natural language interactions with AI assistants like Claude.

The GeneLab Knowledge Graph with data from NASA's GeneLab Data Repository, part of the NASA Open Science Data Repository (OSDR), can be integrated with biomedical knowledge from the SPOKE (Scalable Precision Medicine Open Knowledge Engine) knowledge graph. This integration connects spaceflight experimental results with a comprehensive biological context, including genes, proteins, anatomical structures, pathways, and diseases.

This server is part of the NSF-funded Proto-OKN Project (Prototype Open Knowledge Network). It's an extension of the Neo4j Cypher MCP server.

Features

Natural Language Querying: Ask questions in plain English - no need to write complex graph queries
NASA GeneLab Queries: Ask questions about spaceflight experiments in the NASA GeneLab knowledge graph
Differential Gene Expression Analysis: Find genes that are upregulated or downregulated in spaceflight conditions compared to ground controls
DNA Methylation Data: Access epigenetic changes observed in spaceflight experiments
Multi-Organism Support: Query data across multiple model organisms including mice, rats, and other species used in space research
Tissue-Specific Analysis: Filter results by specific organs, tissues, or cell types
Biomedical Context Integration: Connect spaceflight gene expression changes to pathways, diseases, and other biological knowledge from SPOKE
Federated Queries: Combine data from GeneLab with other Neo4j knowledge graphs for comprehensive biomedical analysis
Multiple Access Methods: Use through Claude Desktop, VS Code with GitHub Copilot, or programmatically via the MCP protocol
Pre-configured Endpoints: Ready-to-use access to both local and remote Neo4j databases containing the GeneLab Knowledge Graph

Prerequisites

Before installing the MCP server, ensure you have:

Operating System: macOS, Linux, or Windows
Client Application: One of the following:
- Claude Desktop with Pro or Max subscription
- VS Code Insiders with GitHub Copilot subscription
Neo4j Knowledge Graphs:
- For a local installation of the GeneLab KG see setup
- For remote access to GeneLab and SPOKE KGs request credentials

Installation

Installation instructions for Claude Desktop and VS Code Insiders

Quick Start

Once configured, you can start querying knowledge graphs through natural language prompts in Claude Desktop or VS Code chat interface.

Select and Configure MCP Tools (Claude Desktop)

From the top menu bar:

1. Select: Claude->Settings->Connectors
2. Click: Configure for the MCP endpoints you want to use
3. Select Tool permissions: Always allow

In the prompt dialog box, click the + button:

1. Turn off Web search
2. Toggle MCP services on/off as needed

Use @kg_name to refer to a specific knowledge graph in chat (for example, @spoke-genelab).

To create a transcript of a chat (see examples below), use the following prompt: Create a chat transcript. The transcript can then be downloaded in .md or .pdf format.

Example Queries

Knowledge Graph Overviews & Class Diagrams

Each link below points to a chat transcript that demonstrates how to generate a knowledge-graph overview and class diagram for a given Neo4j Knowledge Graph.

spoke-genelab

spoke-okn

Troubleshooting

Common Issues

MCP server not appearing in Claude Desktop:

Ensure you've completely quit and restarted Claude Desktop (not just closed the window)
Check that your JSON configuration is valid (attach your config file to a chat and ask it to fix any errors)
Verify that uvx is installed and accessible in your PATH

Connection errors:

Verify the Neo4j endpoint URL is correct and accessible
Some endpoints may have rate limits or temporary downtime

Performance issues:

Complex Cypher queries may take time to execute
Consider breaking down complex queries into smaller parts
Check the endpoint's documentation for query best practices

License

This project is licensed under the BSD 3-Clause License. See the file for details.

Citation

If you use MCP GeneLab in your research, please cite the following works:

@software{rose2025mcp-genelab,
  title={MCP GeneLab Server},
  author={Rose, P.W. and Saravia-Butler, A.M. and Nelson, C.A. and Shi, Y. and Baranzini, S.E.},
  year={2025},
  url={https://github.com/sbl-sdsc/mcp-proto-okn}
}

@software{rose2025spoke-genelab,
  title={NASA SPOKE-GeneLab Knowledge Graph},
  author={Rose, P.W. and Nelson, C.A. and Saravia-Butler, A.M. and Gebre, S.G. and Soman, K. and Grigorev, K.A. and Sanders, L.M. and Costes, S.V. and Baranzini, S.E.},
  year={2025},
  url={https://github.com/BaranziniLab/spoke_genelab}
}

Related Publications

Nelson, C.A., Rose, P.W., Soman, K., Sanders, L.M., Gebre, S.G., Costes, S.V., Baranzini, S.E. (2025). "Nasa Genelab-Knowledge Graph Fabric Enables Deep Biomedical Analysis of Multi-Omics Datasets." NASA Technical Reports, 20250000723. Link
Sanders, L., Costes, S., Soman, K., Rose, P., Nelson, C., Sawyer, A., Gebre, S., Baranzini, S. (2024). "Biomedical Knowledge Graph Capability for Space Biology Knowledge Gain." 45th COSPAR Scientific Assembly, July 13-21, 2024. Link

Acknowledgments

Funding

This work is supported in part by:

National Science Foundation Award #2333819: "Proto-OKN Theme 1: Connecting Biomedical information on Earth and in Space via the SPOKE knowledge graph"

Related Projects

Proto-OKN Project - Prototype Open Knowledge Network initiative
NASA Open Science Data Repository (OSDR) - Repository of multi-modal space life science data
NASA GeneLab Data Repository - GeneLab data repository used to create the GeneLab KG
NASA GeneLab KG - Git Repository for creating the GeneLab KG
Model Context Protocol - AI assistant integration standard
Original Neo4j Cypher MCP server - Base implementation reference

For questions, issues, or contributions, please visit our GitHub repository.