README.md•2.99 kB
# 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
```bash
npm install
npm run build
```
## Usage
### As an MCP Server
Add to your MCP client configuration:
```json
{
"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.
```json
{
"query": "apoptosis",
"ontology": "biological_process",
"size": 10
}
```
#### get_go_term
Get detailed information for a specific GO term.
```json
{
"id": "GO:0006915"
}
```
#### validate_go_id
Validate GO identifier format and check if term exists.
```json
{
"id": "GO:0008150"
}
```
#### get_ontology_stats
Get statistics about GO ontologies (term counts, recent updates).
```json
{
"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
```bash
# Using the search_go_terms tool
{
"query": "apoptosis",
"ontology": "biological_process",
"size": 5,
"include_obsolete": false
}
```
### Get detailed information about a GO term
```bash
# Using the get_go_term tool
{
"id": "GO:0006915"
}
```
### Validate a GO identifier
```bash
# 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:
```bibtex @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}
