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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

Related MCP server: GeoServer MCP Server

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

Fork the repository
Create a feature branch
Make your changes
Add tests if applicable
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}