NCBI Literature Search MCP Server

# 🚀 Claude Desktop Integration Guide Your NCBI Literature Search MCP server is now integrated with Claude Desktop! Here's how to use it. ## ✅ Setup Complete - ✅ NCBI MCP Server configured and tested - ✅ Claude Desktop configuration updated - ✅ Caching enabled for better performance - ✅ Rate limiting configured (10 req/sec with API key) ## 🔄 Next Steps ### 1. Restart Claude Desktop **Important**: You must restart Claude Desktop for the new MCP server to be recognized. 1. Quit Claude Desktop completely 2. Reopen Claude Desktop 3. Look for the 🔧 (tools) icon in your chat interface ### 2. Verify Integration In a new Claude chat, you should see a 🔧 tools icon. If you see it, the integration worked! ## 🔬 How to Use with Claude ### Basic Literature Searches ``` "Search for recent papers on CRISPR gene editing in plants" "Find phylogenetic studies on mammalian evolution from the last 2 years" "Search for computational methods in population genetics" ``` ### Advanced Research Queries ``` "Find review articles about machine learning applications in genomics, published in high-impact journals like Nature or Science" "Search for papers by leading researchers in ancient DNA analysis" "Find recent methods papers for phylogenetic reconstruction algorithms" ``` ### Detailed Article Analysis ``` "Get detailed information including abstracts for the top 5 papers on evolutionary genomics" "Find papers related to this specific study: PMID 12345678" "Search for MeSH terms related to 'phylogenomics' to improve my search strategy" ``` ## 🛠 Available Tools Your Claude now has access to these literature search tools: 1. **search_pubmed** - Primary search tool 2. **get_article_details** - Get full abstracts and metadata 3. **search_mesh_terms** - Find standardized terminology 4. **get_related_articles** - Discover connected research 5. **advanced_search** - Complex multi-criteria searches 6. **batch_search_multiple_queries** - Parallel searches for efficiency 7. **cache_stats** - Monitor performance ## 📖 Example Research Workflows ### Literature Review Workflow 1. Start with broad search: *"Search for computational phylogenetics methods"* 2. Refine with MeSH terms: *"Find MeSH terms for phylogenetics"* 3. Get article details: *"Get abstracts for the top 10 papers from that search"* 4. Find related work: *"Find papers related to PMID [best paper ID]"* ### Staying Current 1. *"Search for new methods in evolutionary biology from the last 6 months"* 2. *"Find recent papers by [favorite researcher name]"* 3. *"Search for software tools published in bioinformatics journals this year"* ### Method Discovery 1. *"Find papers comparing different phylogenetic algorithms"* 2. *"Search for benchmarking studies in computational biology"* 3. *"Find review articles on the latest sequencing technologies"* ## 🚨 Troubleshooting ### If tools don't appear: 1. **Restart Claude Desktop** (most common fix) 2. Check the config file location: `~/Library/Application Support/Claude/claude_desktop_config.json` 3. Verify JSON syntax with: `python3 -m json.tool path/to/config.json` ### If searches fail: 1. Check internet connection 2. Verify NCBI API key is valid 3. Try simpler search terms first ### Performance Issues: 1. Use cache_stats tool to monitor caching 2. Reduce max_results for faster responses 3. Use batch operations for multiple queries ## 📊 Performance Features - **Smart Caching**: Repeated searches are instant - **Rate Limiting**: Respects NCBI's API limits automatically - **Batch Processing**: Handle multiple queries efficiently - **Connection Pooling**: Optimized for sustained use ## 🎯 Pro Tips 1. **Use specific field tags**: `"machine learning"[ti] AND genomics[mh]` 2. **Specify date ranges**: `"from the last 2 years"` or `"published after 2020"` 3. **Combine searches**: Ask for multiple related queries in one request 4. **Get full details**: Always ask for abstracts when you need to read papers 5. **Use MeSH terms**: They help find papers that use different terminology ## 📞 Support If you encounter issues: 1. Check the server logs: `docker-compose logs ncbi-mcp-server` 2. Test standalone: `poetry run python -m src.ncbi_mcp_server.server` 3. Verify configuration in Claude Desktop config file --- **Happy Researching! 🧬📚** Your NCBI MCP server is now ready to accelerate your literature reviews and research discovery with Claude Desktop.