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:
- Build the server:
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:
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:
This server cannot be installed
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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