NCBI Literature Search MCP Server

A Model Context Protocol (MCP) server for searching NCBI databases, designed for researchers across all life sciences and biomedical fields. This server provides seamless access to PubMed's vast collection of 35+ million scientific articles through natural language queries, enabling AI assistants to help with literature reviews, research discovery, and scientific analysis.

Features

🔬 Comprehensive Search: Search PubMed's 35+ million articles across all biological disciplines 📊 Advanced Queries: Support for complex searches with boolean operators, field tags, and filters
🧬 Life Sciences Research: Covers all biological and biomedical fields including genetics, ecology, medicine, and biotechnology 💻 Computational Biology: Perfect for finding bioinformatics methods, algorithms, and computational tools 🔬 Research Applications: Literature reviews, hypothesis generation, method discovery, and staying current with scientific advances 📚 Full Article Details: Get abstracts, author lists, MeSH terms, DOIs, and publication information 🔗 Related Articles: Discover relevant research through NCBI's relationship algorithms 📖 MeSH Integration: Search and utilize Medical Subject Headings for precise terminology

Quick Start

Prerequisites

• Python 3.8 or higher
• Poetry (recommended) - Install Poetry

Setup (5 minutes)

1. Create and initialize project

   mkdir ncbi-mcp-server && cd ncbi-mcp-server
   poetry init
   

   During init, add dependencies: mcp, httpx, typing-extensions

2. Create project structure

   mkdir -p src/ncbi_mcp_server
   # Save server.py code as src/ncbi_mcp_server/server.py
   

3. Install dependencies

   poetry install
   

4. Test the server

   poetry run python src/ncbi_mcp_server/server.py
   

5. Configure Claude Desktop

   Edit your Claude Desktop config file:

   • macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
   • Windows: %APPDATA%/Claude/claude_desktop_config.json
   • Linux: ~/.config/claude/claude_desktop_config.json

   Add this configuration:

   {
     "mcpServers": {
       "ncbi-literature": {
         "command": "poetry",
         "args": ["run", "python", "src/ncbi_mcp_server/server.py"],
         "cwd": "/FULL/PATH/TO/YOUR/ncbi-mcp-server"
       }
     }
   }
   

6. Restart Claude Desktop and start searching!

Alternative Setup Methods

conda env create -f environment.yml
conda activate ncbi-mcp
python server.py

python -m venv venv
source venv/bin/activate  # Linux/macOS
pip install -r requirements.txt
python server.py

Usage Examples

For Evolutionary Biology Research

Search for phylogenetic studies:

"Search for recent phylogenetic analysis papers on mammalian evolution"
→ Uses: search_pubmed with query "phylogenetic analysis[ti] AND mammalian[ti] AND evolution"

Find computational phylogenetics methods:

"Find papers about maximum likelihood methods for phylogenetic reconstruction"
→ Uses: search_pubmed with query "maximum likelihood[ti] AND phylogenetic reconstruction"

Search by specific organism:

"Find recent papers on Drosophila comparative genomics"
→ Uses: search_pubmed with query "Drosophila[ti] AND comparative genomics[ti]"

For Computational Biology Research

Algorithm and method papers:

"Search for machine learning applications in genomics from the last 2 years"
→ Uses: search_pubmed with date_range="730" and query "machine learning AND genomics"

Software and database papers:

"Find papers about new bioinformatics tools for sequence analysis"
→ Uses: search_pubmed with

... [View full README on GitHub](https://github.com/vitorpavinato/ncbi-mcp-server#readme)