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 ```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}