A comprehensive Model Context Protocol server for accessing Gene Ontology data with tools for term search, ontology navigation, gene annotations, and
A comprehensive Model Context Protocol server for accessing Gene Ontology data with tools for term search, ontology navigation, gene annotations, and enrichment analysis. That is what the geneontology mcp server brings to an AI assistant: the same capability, reachable through the Model Context Protocol rather than a separate app or dashboard.
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.
Installation goes through your MCP client rather than a global install: point it at npm on npm and it is fetched when the client starts. The copy-paste blocks for Claude Desktop, Claude Code and Cursor are further down this page.
The server publishes 4 tools. What each one is for:
search_go_terms — Search across Gene Ontology terms by keyword, name, or definitionget_go_term — The get_go_term tool exposed by this servervalidate_go_id — The validate_go_id tool exposed by this serverget_ontology_stats — Get statistics about GO ontologies (term counts, recent updates)Plenty of developer tooling servers cover similar ground. The differences that matter in practice are scope of access and how much setup stands between you and a working tool call. GeneOntology's toolset — search_go_terms, get_go_term, validate_go_id and 1 more — is a fair guide to whether it matches your workflow. It is maintained by Augmented-Nature; worth a glance at recent repository activity before you build anything load-bearing on it.
SyncDev reviews every entry in this directory against the project's own documentation before publishing, and revisits them as servers change.
| Tool | What it does |
|---|---|
| search_go_terms | Search across Gene Ontology terms by keyword, name, or definition. |
| get_go_term | The get_go_term tool exposed by this server. |
| validate_go_id | The validate_go_id tool exposed by this server. |
| get_ontology_stats | Get statistics about GO ontologies (term counts, recent updates). |
{
"mcpServers": {
"geneontology": {
"command": "npx",
"args": ["-y", "npm"]
}
}
}Add to claude_desktop_config.json, then restart Claude Desktop.
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