BioOntology MCP Server

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Unofficial 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.

Features

Search & Discovery

search_terms - Search across ontology terms with advanced filtering options
search_properties - Search ontology properties by labels and IDs
search_ontologies - Find ontologies by name, description, or domain
get_ontology_info - Get detailed information about specific ontologies

Text Analysis

annotate_text - Analyze text and identify relevant ontology terms
recommend_ontologies - Get ontology recommendations for text or keywords
batch_annotate - Process multiple texts for annotation efficiently

get_class_info - Get detailed information about ontology classes

Analytics & Metadata

get_ontology_metrics - Get usage statistics and quality metrics
get_analytics_data - Get visitor statistics and popularity trends

Installation

Clone or download this server
Install dependencies:
npm install
Build the server:
npm run build

Configuration

You need a BioOntology API key to use this server. Get one from BioPortal:

Create an account at https://bioportal.bioontology.org/
Generate an API key from your account settings
Set the environment variable:
export BIOONTOLOGY_API_KEY=your_api_key_here

Usage

Running the Server

node build/index.js

The server runs on stdio and implements the MCP protocol for communication with MCP-compatible clients.

Resource Templates

The server provides several resource templates for direct data access:

bioontology://ontology/{acronym} - Complete ontology information
bioontology://class/{ontology}/{class_id} - Ontology class details
bioontology://search/{query} - Term search results
bioontology://annotations/{text} - Text annotation results
bioontology://recommendations/{input} - Ontology recommendations
bioontology://analytics/{ontology} - Analytics data

Example Tool Calls

Search for terms:

{
  "tool": "search_terms",
  "arguments": {
    "query": "diabetes",
    "ontologies": "NCIT,DOID",
    "require_definitions": true,
    "pagesize": 10
  }
}

Annotate text:

{
  "tool": "annotate_text",
  "arguments": {
    "text": "The patient has diabetes mellitus and hypertension",
    "ontologies": "NCIT,DOID,HP",
    "longest_only": true
  }
}

Get ontology recommendations:

{
  "tool": "recommend_ontologies",
  "arguments": {
    "input": "cancer treatment protocols",
    "input_type": 1,
    "output_type": 1
  }
}

Batch annotate multiple texts:

{
  "tool": "batch_annotate",
  "arguments": {
    "texts": ["diabetes mellitus", "cardiac arrest", "lung cancer"],
    "ontologies": "NCIT",
    "longest_only": true
  }
}

Supported Ontologies

The server works with all ontologies available in BioPortal (1,200+), including:

Medical/Clinical:

NCIT - NCI Thesaurus (cancer terminology)
DOID - Disease Ontology
HP - Human Phenotype Ontology
MESH - Medical Subject Headings

Biological/Chemical:

GO - Gene Ontology
UBERON - Anatomy ontology
CHEBI - Chemical entities of biological interest

And 1,190+ more specialized ontologies

Integration with MCP Clients

This server is compatible with any MCP-enabled client. Popular options include:

Claude Desktop - Add to your MCP configuration
VSCode Extensions - Use with MCP-compatible extensions
Custom Applications - Integrate via the MCP protocol

MCP Configuration Example

Add to your MCP client configuration:

{
  "servers": {
    "bioontology": {
      "command": "node",
      "args": ["/path/to/bioontology-server/build/index.js"],
      "env": {
        "BIOONTOLOGY_API_KEY": "your_api_key_here"
      }
    }
  }
}

Advanced Features

Input Validation

Comprehensive parameter validation with proper error messages
Type checking for all inputs
Range validation for numeric parameters
Enum validation for restricted values

Error Handling

Graceful handling of API errors
Structured error responses
Network timeout management
Authentication error reporting

Performance

Efficient API request handling
Proper timeout management
Memory usage optimization
Concurrent request support

API Documentation

For detailed BioOntology API documentation, see: https://data.bioontology.org/documentation

Production Use

This server has been thoroughly tested and is ready for production use. It provides:

Reliable API integration with robust error handling
Comprehensive input validation for all tools
Full MCP protocol compliance for seamless integration
Support for 1,200+ ontologies across all biological domains
High performance with optimized response times

License

MIT License - see LICENSE file for details.

Citation

If you use this project in your research or publications, please cite it as follows:

Install Server

HTTP connection URL

security – no known vulnerabilities

license - permissive license

quality - confirmed to work

How are these scores calculated?

remote-capable server

The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.

Tools

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