vitorpavinato/ncbi-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**
During init, add dependencies: mcp, httpx, typing-extensions
2. **Create project structure**
3. **Install dependencies**
4. **Test the server**
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:
6. **Restart Claude Desktop** and start searching!
Alternative Setup Methods
Click to expand alternative installation methods
**Conda Environment**
**Standard pip + venv**
Usage Examples
For Evolutionary Biology Research
**Search for phylogenetic studies:**
**Find computational phylogenetics methods:**
**Search by specific organism:**
For Computational Biology Research
**Algorithm and method papers:**
**Software and database papers:**
Advanced Search Examples
**Multi-criteria search:**
**Author-specific searches:**
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