ncbi-mcp

# NCBI Model Context Protocol (MCP) A Python implementation of the Model Context Protocol for interacting with NCBI databases. ## Setup 1. Clone this repository 2. Install dependencies: ``` pip install -r requirements.txt ``` 3. Create a `.env` file with your NCBI API key: ``` NCBI_API_KEY=your_api_key_here NCBI_EMAIL=your_email@example.com ``` ## Running the MCP Server ``` python ncbi_mcp.py ``` ## Using with Cursor/Claude Once the MCP server is running, you can interact with it using natural language in Cursor/Claude. ### Using Natural Language Queries You can use natural language to perform searches and retrieve information: ``` tools/call { "name": "nlp-query", "arguments": { "query": "Find research articles about BRCA1" } } ``` Or more simply, just use the query directly: ``` @ncbi-mcp Find research articles about BRCA1 ``` ### Example Queries Here are some example queries you can try: 1. Search for scientific articles: ``` @ncbi-mcp Find the latest research on COVID-19 vaccines ``` 2. Get gene information: ``` @ncbi-mcp Tell me about the BRCA1 gene ``` 3. Fetch genome information: ``` @ncbi-mcp Get genome information for Homo sapiens ``` 4. Fetch a specific record: ``` @ncbi-mcp Get gene ID 70 ``` ## Testing To test the MCP server with various queries, you can use the included test files: ``` # Test natural language query functionality (default) .\run_test.bat # Test all tools .\run_test.bat all # Test specific test file .\run_test.bat test_all_tools.jsonl ``` The test script will: 1. Start the MCP server in background 2. Send test requests from the specified file 3. Wait for a few seconds to allow processing 4. Terminate the server and display the output This approach is used because the MCP server is designed to run continuously as a service. For manual testing without automatic termination, you can use: ``` # Run manually with any test file type test_nlp_query.jsonl | python ncbi_mcp.py ``` The test files contain example JSON-RPC requests that simulate how Cursor/Claude would interact with the MCP server. ## Advanced Usage For more advanced usage, you can directly call the specific tools: ### Search NCBI Databases ``` tools/call { "name": "ncbi-search", "arguments": { "database": "pubmed", "term": "BRCA1", "filters": { "organism": "Homo sapiens", "date_range": { "start": "2020" } } } } ``` ### Fetch NCBI Records ``` tools/call { "name": "ncbi-fetch", "arguments": { "database": "gene", "ids": ["70"], "rettype": "gb" } } ``` ### Get Gene Information ``` tools/call { "name": "get_gene_info", "arguments": { "gene_id": "672" } } ``` ### Get Genome Information ``` tools/call { "name": "get_genome_info", "arguments": { "organism": "Homo sapiens", "reference": true } } ``` ## License Apache-2.0