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BioOntology MCP Server

@Augmented-Nature

Repository

Basic information

Category

Other

Transports

stdio

Author

Augmented-Nature

Submitted by

Moudather Chelbi

About BioOntology MCP Server

A production-ready Model Context Protocol (MCP) server that provides comprehensive access to the BioOntology API for searching, annotating, and exploring over 1,200 biological ontologies.

#bioontology#mcp-server#biological-ontologies

BioOntology MCP Server config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "BioOntology-MCP-Server": {
      "command": "node",
      "args": [
        "build/index.js"
      ]
    }
  }
}

BioOntology MCP Server tools

Tool list not available yet

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We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

What is BioOntology MCP Server?

BioOntology MCP Server is a production-ready Model Context Protocol server that provides comprehensive access to the BioOntology API for searching, annotating, and exploring over 1,200 biological ontologies. It is designed for researchers, clinicians, and developers who need to integrate ontology lookup, text annotation, and recommendations into MCP-compatible clients.

How to use BioOntology MCP Server?

Install dependencies with npm install, build with npm run build, and set the BIOONTOLOGY_API_KEY environment variable with an API key from BioPortal. Run the server with node build/index.js. The server communicates via stdio and can be integrated into MCP clients like Claude Desktop or VSCode extensions by configuring the command and environment.

Key features of BioOntology MCP Server

  • Search ontology terms, properties, and ontologies
  • Annotate text and batch process multiple texts
  • Recommend ontologies based on keywords
  • Retrieve class details and ontology metrics
  • Access analytics and popularity trends
  • Resource templates for direct data access

Use cases of BioOntology MCP Server

  • Clinical researchers annotating patient records with standard ontology terms
  • Bioinformaticians searching for ontology terms across 1,200+ ontologies
  • Developers building ontology-aware applications with text annotation
  • Educators exploring ontology classes and relationships
  • Analysts gathering usage statistics and popularity trends

Frequently asked questions

1

What is the BioOntology API and how do I get an API key?

The server requires a BioOntology API key from BioPortal. Create an account at https://bioportal.bioontology.org/ and generate an API key from account settings.

2

What ontologies are supported?

Over 1,200 ontologies from BioPortal, including NCIT, DOID, HP, MESH, GO, UBERON, CHEBI, and many more specialized ontologies.

3

How do I integrate this server with a client like Claude Desktop?

Add a configuration entry with the command `node`, arguments pointing to the build/index.js, and set the `BIOONTOLOGY_API_KEY` environment variable in the `env` object.

4

What are the resource templates available?

The server provides resource templates for ontology info, class details, search results, text annotations, ontology recommendations, and analytics data, accessible via URIs like `bioontology://ontology/{acronym}`.

5

Is this server production-ready?

Yes, it has been thoroughly tested and includes reliable API integration, comprehensive input validation, full MCP protocol compliance, and high performance.

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