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
- 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 informationbioontology://class/{ontology}/{class_id}- Ontology class detailsbioontology://search/{query}- Term search resultsbioontology://annotations/{text}- Text annotation resultsbioontology://recommendations/{input}- Ontology recommendationsbioontology://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},
}