Bioontology MCP Server

🚀 Unofficial BioOntology MCP Server

This is a production-ready Model Context Protocol (MCP) server. It offers comprehensive access to the BioOntology API, enabling users to search, annotate, and explore 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 Examples

Basic 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.

Advanced Usage

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"
      }
    }
  }
}

🔧 Technical Details

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},
}