home / mcp / geneontology mcp server

GeneOntology 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.

Installation

Add the following to your MCP client configuration file.

Configuration

View docs

{
  "mcpServers": {
    "augmented-nature-geneontology-mcp-server": {
      "command": "node",
      "args": [
        "/path/to/go-server/build/index.js"
      ]
    }
  }
}

You can access Gene Ontology data via a dedicated MCP Server that exposes GO terms, annotations, and ontology statistics through a standardized, programmable interface. This server enables AI systems to perform ontology-based analyses, gene annotation research, and functional enrichment studies with stable, schema-driven access.

How to use

Configure your MCP client to connect to the GO MCP Server. You can run the server as a local process and point your client to the executable, which is started with Node.js and the built bundle.

{
  "mcpServers": {
    "go-server": {
      "command": "node",
      "args": ["/path/to/go-server/build/index.js"]
    }
  }
}

How to access core capabilities

Use the server to search GO terms, navigate their hierarchy, retrieve gene annotations, validate GO identifiers, and obtain ontology statistics. The server exposes a set of resource endpoints that your client can request to perform these actions.

Typical usage pattern

1) Start the GO MCP Server using the command shown in the configuration snippet. 2) Add the server as a data source in your MCP client configuration. 3) Invoke the available tools and endpoints to query terms, fetch annotations, or validate identifiers. 4) Handle errors such as invalid identifiers, missing terms, API timeouts, and network issues with the client’s retry and error-handling logic.

Resource templates

You can reference common resources with helper paths that map to GO data. Examples include complete term data, gene annotations, search results, and term hierarchies.

Available tools

search_go_terms

Search GO terms by keyword, name, or definition across ontology categories.

get_go_term

Retrieve detailed information for a specific GO term by its identifier.

validate_go_id

Validate GO identifier format and verify term existence.

get_ontology_stats

Fetch statistics about GO ontologies, including term counts and recent updates.