Provides comprehensive access to the BioOntology API for searching, annotating, and exploring over 1,200 biological ontologies, including features for term searching, text annotation, ontology navigation, and analytics.
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 installBuild 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
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:
Annotate text:
Get ontology recommendations:
Batch annotate multiple texts:
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:
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:
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
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.
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