Geneontology Mcp Server

What is Geneontology Mcp Server?

Geneontology Mcp Server is an unofficial Model Context Protocol server that provides AI systems with access to Gene Ontology (GO) data. It enables ontology-based analysis, gene annotation research, and functional enrichment studies by integrating with the QuickGO API and the GO Consortium.

How to use Geneontology Mcp Server?

Install with npm install && npm run build, then add the built index.js to your MCP client configuration as a command‑line server. Use the provided tools (search_go_terms, get_go_term, validate_go_id, get_ontology_stats) and resource templates (go://term/{id}, go://annotations/{gene}, go://search/{query}, go://hierarchy/{id}) to interact with GO data.

Key features of Geneontology Mcp Server

• Search GO terms by keyword, name, or definition
• Retrieve detailed information for a specific GO term
• Validate GO identifiers and check term existence
• Navigate hierarchical relationships between ontology terms
• Access GO annotations for genes and proteins
• Obtain ontology statistics and metadata

Use cases of Geneontology Mcp Server

• AI‑powered literature review requiring GO term lookups and definitions
• Automated functional enrichment analysis of gene lists
• Validating GO identifiers in large‑scale bioinformatics pipelines
• Exploring ontology hierarchies to identify parent‑child term relationships
• Retrieving gene annotations for genomic research and curation

FAQ from Geneontology Mcp Server

What data sources does Geneontology Mcp Server use?

It integrates with the QuickGO API (primary source), the official GO Consortium, and the AmiGO browsing interface.

What are the dependencies for running Geneontology Mcp Server?

A Node.js runtime and npm are required. The server is installed via npm install and built with npm run build.

How does Geneontology Mcp Server handle errors?

The server includes comprehensive error handling for invalid GO identifiers, missing terms, API timeouts, network errors, and malformed requests.

Is this an official Gene Ontology server?

No, Geneontology Mcp Server is an unofficial community project. It is not maintained by the GO Consortium or QuickGO.

What transport does Geneontology Mcp Server use?

It is configured as a standard MCP server using a command‑line invocation (node /path/to/build/index.js), which typically uses stdio transport.