Geneontology Mcp Server

Name: Geneontology Mcp Server
Author: Augmented-Nature

@Augmented-Nature

About 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.

#geneontology #mcp-server #ontology-analysis

Basic information

Config

No standard config provided

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Repository

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Overview

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.

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