BioOntology MCP Server

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

Ontology Navigation

• 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

1. Clone or download this server
2. Install dependencies:

   npm install
   

3. Build the server:

   npm run build
   

Configuration

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

1. Create an account at https://bioportal.bioontology.org/
2. Generate an API key from your account settings
3. 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:

@misc{yourproject2025,
  author       = {Moudather Chelbi},
  title        = {Augmented Nature BioOntology MCP Server},
  year         = {2025},
  howpublished = {https://github.com/Augmented-Nature/BioOntology-MCP-Server},
}