GeneOntology

This MCP server provides access to Gene Ontology (GO) data, enabling AI systems to perform ontology-based analysis, gene annotation retrieval, and term validation. It exposes tools for searching GO terms, fetching detailed term information, validating GO identifiers, and obtaining ontology-wide statistics. Use the go-server entry in your MCP client configuration to connect, then invoke the provided tools (search_go_terms, get_go_term, validate_go_id, and get_ontology_stats) to interact with GO data. The resource templates (go://term, go://annotations, go://search, go://hierarchy) help standardize how you request data and navigate the ontology hierarchy.

Prerequisites:

• Node.js and npm installed on your system.

Install and build:

1. git clone <repository-url> // if you haven't already
2. cd GeneOntology-MCP-Server
3. npm install
4. npm run build

Run locally (example):

• Ensure you have a Node environment and that build/index.js exists after npm run build.
• Start the server as part of your MCP network configuration, for example by launching the MCP bridge or wrapper that loads the built index.js entry point.

Notes:

• The server expects to be accessed via the MCP protocol through the configured command and path (see mcp_config).

Tips and common issues:

• Ensure the build output path matches the path used in the mcp_config (index.js under build is typical after npm run build).
• If GO data sources require credentials or API keys (e.g., QuickGO), set the appropriate environment variables as needed by your deployment (not detailed in this README).
• Validate GO IDs using validate_go_id to quickly catch malformed identifiers before querying detailed term data.
• Monitor for API rate limits if the server relies on external services (QuickGO/GO Consortium) and implement retry/backoff as needed in your client.
• If you modify data sources or endpoints, update get_ontology_stats and related documentation to reflect new statistics or fields.

Environment variable placeholder examples (if needed):

• GO_API_KEY=your-quickgo-api-key
• GO_BASE_URL=https://www.ebi.ac.uk/QuickGO/api

Configuration tip: keep the mcpServers entry consistent with your MCP infrastructure naming conventions (e.g., server-name: go-server).