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.

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

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

Examples

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"
}

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

Citation

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

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