Geneontology MCP Server

🚀 Unofficial Gene Ontology MCP Server

A comprehensive Model Context Protocol server for accessing Gene Ontology (GO) data, enabling AI systems to perform ontology-based analysis, gene annotation research, and functional enrichment studies.

🚀 Quick Start

This Unofficial Gene Ontology MCP Server allows you to access Gene Ontology (GO) data. You can perform term searches, ontology navigation, access gene annotations, and more. Below are the installation and usage instructions.

✨ Features

• Term Search & Lookup: Search GO terms by keyword, name, or definition
• Ontology Navigation: Explore hierarchical relationships between terms
• Gene Annotations: Access GO annotations for genes and proteins
• Validation: Validate GO identifiers and check term existence
• Statistics: Get comprehensive ontology statistics and metadata

📦 Installation

npm install
npm run build

💻 Usage Examples

As an MCP Server

Add to your MCP client configuration:

{
  "mcpServers": {
    "go-server": {
      "command": "node",
      "args": ["/path/to/go-server/build/index.js"]
    }
  }
}

Available Tools

search_go_terms

Search across Gene Ontology terms by keyword, name, or definition.

{
  "query": "apoptosis",
  "ontology": "biological_process",
  "size": 10
}

get_go_term

Get detailed information for a specific GO term.

{
  "id": "GO:0006915"
}

validate_go_id

Validate GO identifier format and check if term exists.

{
  "id": "GO:0008150"
}

get_ontology_stats

Get statistics about GO ontologies (term counts, recent updates).

{
  "ontology": "all"
}

Resource Templates

• go://term/{id} - Complete GO term information
• go://annotations/{gene} - Gene annotations
• go://search/{query} - Search results
• go://hierarchy/{id} - Term hierarchy relationships

Basic Usage

Search for apoptosis-related terms

# Using the search_go_terms tool
{
  "query": "apoptosis",
  "ontology": "biological_process",
  "size": 5,
  "include_obsolete": false
}

Get detailed information about a GO term

# Using the get_go_term tool
{
  "id": "GO:0006915"
}

Validate a GO identifier

# Using the validate_go_id tool
{
  "id": "GO:0008150"
}

📚 Documentation

Data Sources

This server integrates with:

• QuickGO API (https://www.ebi.ac.uk/QuickGO/) - Primary data source
• GO Consortium (https://geneontology.org/) - Official Gene Ontology
• AmiGO (http://amigo.geneontology.org/) - Additional browsing interface

Error Handling

The server includes comprehensive error handling for:

• Invalid GO identifiers
• Missing terms
• API timeouts
• Network errors
• Malformed requests

🤝 Contributing

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Add tests if applicable
5. Submit a pull request

📄 License

If you use this project in your research or publications, please cite it as follows:

@misc{geneontologymcp2025, 
author = {Moudather Chelbi},
title = {GeneOntology MCP Server},
year = {2025},
howpublished = {https://github.com/Augmented-Nature/GeneOntology-MCP-Server},
note = {Accessed: 2025-06-29}
}