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)
-
Create and initialize project
mkdir ncbi-mcp-server && cd ncbi-mcp-server poetry initDuring init, add dependencies:
mcp,httpx,typing-extensions -
Create project structure
mkdir -p src/ncbi_mcp_server # Save server.py code as src/ncbi_mcp_server/server.py -
Install dependencies
poetry install -
Test the server
poetry run python src/ncbi_mcp_server/server.py -
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" } } } - macOS:
-
Restart Claude Desktop and start searching!
Alternative Setup Methods
Click to expand alternative installation methods
Conda Environment
conda env create -f environment.yml
conda activate ncbi-mcp
python server.py
Standard pip + venv
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 query "bioinformatics[ti] AND software[ti] AND sequence analysis"
Advanced Search Examples
Multi-criteria search:
"Find review articles about CRISPR applications in evolutionary studies published in Nature or Science"
→ Uses: advanced_search with terms=["CRISPR", "evolution"], publication_types=["Review"], journals=["Nature", "Science"]
Author-specific searches:
"Find recent papers by researchers working on ancient DNA and phylogenomics"
→ Uses: search_pubmed with query "ancient DNA[ti] AND phylogenomics[ti]"
Tool Reference
search_pubmed
Primary search tool for PubMed database
- query: Search terms (supports field tags like
[ti]for title,[au]for author,[mh]for MeSH terms) - max_results: Number of results (1-100, default: 20)
- sort: Sort by "relevance", "pub_date", "author", or "journal"
- date_range: Limit to recent articles ("30", "90", "365", "1095" days)
Examples:
"CRISPR[ti] AND evolution"- CRISPR in title AND evolution anywhere"phylogenetic analysis[mh]"- Using MeSH term for phylogenetic analysis"computational biology AND machine learning"- Boolean search
get_article_details
Fetch complete information for specific articles
- pmids: List of PubMed IDs (up to 50)
Returns full abstracts, author lists, MeSH terms, DOI, publication details
search_mesh_terms
Find standardized Medical Subject Headings
- term: Term to search in MeSH database
Helps discover related concepts and improve search precision
get_related_articles
Discover articles related to a specific paper
- pmid: PubMed ID of reference article
- max_results: Number of related articles (1-50, default: 10)
Perfect for literature reviews and finding relevant research
advanced_search
Complex searches with multiple criteria
- terms: List of search terms to combine
- operator: "AND", "OR", or "NOT" to combine terms
- authors: List of author names
- journals: List of journal names
- publication_types: "Research Article", "Review", "Meta-Analysis", etc.
- date_from/date_to: Date range in YYYY/MM/DD format
- max_results: Number of results (1-100, default: 20)
Analytics & Performance Monitoring
The NCBI MCP Server includes comprehensive analytics to help you understand your research patterns and optimize performance.
Analytics Tools
get_analytics_summary
Get comprehensive analytics overview
"Show me my research analytics summary"
Returns:
- Total requests and uptime
- Operation breakdown (searches, fetches, etc.)
- Cache performance metrics
- Recent activity and error rates
- System health indicators
get_detailed_metrics
Detailed performance metrics for specific time periods
"Get detailed metrics for the last 24 hours"
- hours: Time period to analyze (default: 24)
- Operation-specific performance data
- Timeline analysis with hourly breakdowns
- Error rates and response times per operation
reset_analytics
Reset analytics data (use with caution)
"Reset all analytics data"
Note: This permanently clears all collected metrics.
What's Tracked
Usage Patterns:
- Search queries and frequency
- Most used operations
- Unique vs. repeated queries
- Peak usage periods
Performance Metrics:
- Response times for each operation
- Cache hit/miss rates
- Error rates and types
- Rate limiting efficiency
Research Insights:
- Popular search terms and patterns
- Research workflow analysis
- Literature access patterns
- Most accessed journals and topics
Deployment
Quick Start
-
Configure credentials:
cp .env.example .env # Edit .env with your NCBI email and API key -
Choose deployment method:
# Local development ./deploy.sh local # Docker deployment ./deploy.sh docker # Production deployment ./deploy.sh production
Deployment Options
1. Local Development
Perfect for development and testing:
poetry install
poetry run python -m src.ncbi_mcp_server.server
2. Docker Deployment
Recommended for most users with two options:
Full setup with Redis (recommended):
# Copy and configure environment
cp .env.example .env
# Edit .env with your NCBI email and API key
# Start all services
docker-compose up -d
Simple setup without Redis:
# For basic usage without Redis dependencies
cp .env.example .env
# Edit .env with your NCBI email
docker-compose -f docker-compose.simple.yml up -d
Full setup includes:
- NCBI MCP Server container
- Redis cache for performance
- Redis Commander UI (http://localhost:8081)
Simple setup includes:
- NCBI MCP Server container only
- In-memory caching (no persistence)
3. Production Deployment
For production environments:
# Configure production settings
cp .env.production .env
# Edit with production values
# Deploy
./deploy.sh production
Monitoring
Docker logs:
docker-compose logs -f ncbi-mcp-server
Cache monitoring:
- Redis Commander: http://localhost:8081
- Cache stats via MCP tool:
cache_stats()
Health checks:
# Test server health
curl http://localhost:8000/health
# Test via MCP
python -c "from src.ncbi_mcp_server.server import cache_stats; import asyncio; print(asyncio.run(cache_stats()))"
Configuration
NCBI API Key (Optional but Recommended)
For higher rate limits and better performance:
- Register at NCBI: https://www.ncbi.nlm.nih.gov/account/
- Get API key: https://www.ncbi.nlm.nih.gov/account/settings/
- Add to server code in
src/ncbi_mcp_server/server.py:
# Replace the line: ncbi_client = NCBIClient()
# With:
ncbi_client = NCBIClient(
email="your.email@university.edu",
api_key="your_api_key_here"
)
Rate Limits
- Without API key: 3 requests/second
- With API key: 10 requests/second
- With API key + email: Higher limits for bulk requests
Development Workflow
Poetry Commands
poetry shell # Activate virtual environment
poetry add package # Add new dependency
poetry remove package # Remove dependency
poetry update # Update all dependencies
poetry run python ... # Run commands in environment
poetry build # Create distribution packages
Code Quality (if you added dev dependencies)
poetry add --group dev black mypy pytest isort flake8
poetry run black . # Format code
poetry run mypy . # Type checking
poetry run pytest # Run tests
poetry run isort . # Sort imports
Sharing with Colleagues
# They just need:
git clone your-repo
cd ncbi-mcp-server
poetry install
# Everything works identically!
Field Tags for Advanced Searches
PubMed supports many field tags for precise searching:
[ti]- Title[tiab]- Title and Abstract[au]- Author[mh]- MeSH Terms[journal]- Journal Name[pdat]- Publication Date[pt]- Publication Type[lang]- Language[sb]- Subset (e.g., medline, pubmed)
Example Advanced Queries:
"machine learning"[ti] AND "phylogen*"[tiab] AND "2020"[pdat]:"2024"[pdat]
evolutionary[mh] AND computational[ti] AND (genomics[tiab] OR proteomics[tiab])
"ancient DNA"[ti] AND (paleogenomics[mh] OR phylogenomics[tiab])
Research Workflow Examples
Literature Review Workflow
- Start broad:
search_pubmed("computational phylogenetics") - Refine with MeSH:
search_mesh_terms("phylogenetics") - Find key papers: Use publication dates and journal filters
- Explore connections:
get_related_articles(pmid="key_paper_id") - Deep dive:
get_article_details(pmids=["12345", "67890"])
Staying Current
- Recent methods:
search_pubmed("new methods", date_range="90") - Follow key authors:
search_pubmed("author_name[au]", sort="pub_date") - Track specific topics:
advanced_searchwith your research keywords
Method Discovery
- Algorithm papers:
search_pubmed("algorithm[ti] AND your_field") - Software tools:
search_pubmed("software[ti] OR tool[ti] AND bioinformatics") - Benchmarking:
search_pubmed("comparison[ti] OR benchmark[ti]")
Troubleshooting
Common Issues
Server won't start:
- Check Python version (3.8+ required)
- Install dependencies:
pip install -r requirements.txt - Verify file permissions
No search results:
- Check query syntax (use proper field tags)
- Try broader search terms
- Verify internet connection
Rate limit errors:
- Add delays between requests
- Get NCBI API key for higher limits
- Consider searching fewer results per query
XML parsing errors:
- Usually temporary NCBI server issues
- Retry after a few seconds
- Check NCBI status: https://www.ncbi.nlm.nih.gov/
Getting Help
- NCBI E-utilities documentation: https://www.ncbi.nlm.nih.gov/books/NBK25499/
- PubMed search tips: https://pubmed.ncbi.nlm.nih.gov/help/
- MeSH database: https://www.ncbi.nlm.nih.gov/mesh/
Contributing
This MCP server is designed to grow with the research community. Ideas for enhancement:
- Additional databases: PMC, BioRxiv, databases beyond NCBI
- Citation analysis: Track paper impact and citation networks
- Export formats: BibTeX, EndNote, RIS for reference managers
- Saved searches: Persistent search profiles and alerts
- Full-text integration: When available through PMC
License
This project is open source. Feel free to modify and distribute according to your institution's policies.
Perfect for researchers in:
- Evolutionary Biology & Phylogenetics
- Computational Biology & Bioinformatics
- Molecular Evolution & Population Genetics
- Comparative Genomics & Proteomics
- Systems Biology & Network Analysis
- Biostatistics & Mathematical Biology
- Ancient DNA & Paleogenomics
- Conservation Genetics & Ecology
Start exploring the vast world of biological literature with powerful, precise searches!