What is Bioontology Mcp Server

BioOntology-MCP-Server is an unofficial Model Context Protocol (MCP) server designed to provide comprehensive access to the BioOntology API, enabling users to search, annotate, and explore over 1,200 biological ontologies.

Use cases

Use cases include searching for specific biological terms, annotating research texts with relevant ontologies, recommending ontologies based on keywords, and analyzing visitor statistics for ontology usage.

How to use

To use BioOntology-MCP-Server, clone or download the server, install the necessary dependencies using ‘npm install’, build the server with ‘npm run build’, and run it using ‘node build/index.js’. Ensure you have a BioOntology API key set as an environment variable.

Key features

Key features include advanced search and discovery options for ontology terms and properties, text analysis for annotating relevant ontology terms, ontology navigation for detailed class information, and analytics for usage statistics and quality metrics.

Where to use

BioOntology-MCP-Server can be used in various fields such as bioinformatics, computational biology, and any domain requiring access to biological ontologies for research, data analysis, and knowledge discovery.

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.