BioMCP

# BioMCP: AI-Powered Biomedical Research [](https://github.com/genomoncology/biomcp/tags) [](https://github.com/genomoncology/biomcp/actions/workflows/main.yml?query=branch%3Amain) [](https://img.shields.io/github/license/genomoncology/biomcp) **Transform how you search and analyze biomedical data** with BioMCP - a powerful tool that connects AI assistants and researchers to critical biomedical databases through natural language. ### Built and Maintained by <a href="https://www.genomoncology.com"><img src="./assets/logo.png" width=200 valign="middle" /></a> <div class="announcement-banner"> <div class="announcement-content"> <h2> <span class="badge-new">NEW</span> Remote BioMCP Now Available! </h2> <p>Connect to BioMCP instantly through Claude - no installation required!</p> <div class="announcement-features"> <div class="feature-item"> <strong>🚀 Instant Access</strong> <span>Start using BioMCP in under 2 minutes</span> </div> <div class="feature-item"> <strong>☁️ Cloud-Powered</strong> <span>Always up-to-date with latest features</span> </div> <div class="feature-item"> <strong>🔒 Secure Auth</strong> <span>Google OAuth authentication</span> </div> <div class="feature-item"> <strong>🛠️ 23+ Tools</strong> <span>Full suite of biomedical research tools</span> </div> </div> <a href="tutorials/remote-connection/" class="cta-button"> Connect to Remote BioMCP Now </a> </div> </div> ## What Can You Do with BioMCP? ### Search Research Literature Find articles about genes, variants, diseases, and drugs with automatic cancer genomics data from cBioPortal ```bash biomcp article search --gene BRAF --disease melanoma ``` ### Discover Clinical Trials Search active trials by condition, location, phase, and eligibility criteria including genetic biomarkers ```bash biomcp trial search --condition "lung cancer" --status RECRUITING ``` ### Analyze Genetic Variants Query variant databases, predict effects, and understand clinical significance ```bash biomcp variant search --gene TP53 --significance pathogenic ``` ### AI-Powered Analysis Use with Claude Desktop for conversational biomedical research with sequential thinking ```python # Claude automatically uses BioMCP tools "What BRAF mutations are found in melanoma?" ``` ## 5-Minute Quick Start ### Choose Your Interface === "Claude Desktop (Recommended)" **Best for**: Conversational research, complex queries, AI-assisted analysis 1. **Install Claude Desktop** from [claude.ai/desktop](https://claude.ai/desktop) 2. **Configure BioMCP**: ```json { "mcpServers": { "biomcp": { "command": "uv", "args": [ "run", "--with", "biomcp-python", "biomcp", "run" ] } } } ``` 3. **Start researching**: Ask Claude about any biomedical topic! [Full Claude Desktop Guide →](getting-started/02-claude-desktop-integration.md) === "Command Line" **Best for**: Direct queries, scripting, automation 1. **Install BioMCP**: ```bash # Using uv (recommended) uv tool install biomcp # Or using pip pip install biomcp-python ``` 2. **Run your first search**: ```bash biomcp article search \ --gene BRAF --disease melanoma \ --limit 5 ``` [CLI Reference →](user-guides/01-command-line-interface.md) === "Python SDK" **Best for**: Integration, custom applications, bulk operations 1. **Install the package**: ```bash pip install biomcp-python ``` 2. **Use in your code**: ```python from biomcp import BioMCPClient async with BioMCPClient() as client: articles = await client.articles.search( genes=["BRAF"], diseases=["melanoma"] ) ``` [Python SDK Docs →](apis/python-sdk.md) ## Key Features ### Unified Search Across Databases - **PubMed/PubTator3**: 30M+ research articles with entity recognition - **ClinicalTrials.gov**: 400K+ clinical trials worldwide - **MyVariant.info**: Comprehensive variant annotations - **cBioPortal**: Automatic cancer genomics integration ### Intelligent Query Processing - Natural language to structured queries - Automatic synonym expansion - OR logic support for flexible matching - Cross-domain relationship discovery ### Built for AI Integration - 24 specialized MCP tools - Sequential thinking for complex analysis - Streaming responses for real-time updates - Context preservation across queries [Explore All Features →](concepts/01-what-is-biomcp.md) ## Learn by Example ### Find Articles About a Specific Mutation ```bash # Search for BRAF V600E mutations biomcp article search --gene BRAF \ --keyword "V600E|p.V600E|c.1799T>A" ``` ### Discover Trials Near You ```bash # Find cancer trials in Boston area biomcp trial search --condition cancer \ --latitude 42.3601 --longitude -71.0589 \ --distance 50 ``` ### Get Gene Information ```bash # Get comprehensive gene data biomcp gene get TP53 ``` [More Examples →](tutorials/biothings-prompts.md) ## Popular Workflows ### Literature Review Systematic search across papers, preprints, and clinical trials [Workflow Guide →](workflows/all-workflows.md#1-literature-review-workflow) ### Variant Interpretation From variant ID to clinical significance and treatment implications [Workflow Guide →](workflows/all-workflows.md#3-variant-interpretation-workflow) ### Trial Matching Find eligible trials based on patient criteria and biomarkers [Workflow Guide →](workflows/all-workflows.md#2-clinical-trial-matching-workflow) ### Drug Research Connect drugs to targets, trials, and research literature [Workflow Guide →](workflows/all-workflows.md) ## Advanced Features - **[NCI Integration](getting-started/03-authentication-and-api-keys.md#nci-clinical-trials-api)**: Enhanced cancer trial search with biomarker filtering - **[AlphaGenome](how-to-guides/04-predict-variant-effects-with-alphagenome.md)**: Predict variant effects on gene regulation - **[BigQuery Logging](how-to-guides/05-logging-and-monitoring-with-bigquery.md)**: Monitor usage and performance - **[HTTP Server Mode](developer-guides/01-server-deployment.md)**: Deploy as a service ## Documentation - **[Getting Started](getting-started/01-quickstart-cli.md)** - Installation and first steps - **[User Guides](user-guides/01-command-line-interface.md)** - Detailed usage instructions - **[API Reference](apis/overview.md)** - Technical documentation - **[FAQ](faq-condensed.md)** - Quick answers to common questions ## Community & Support - **GitHub**: [github.com/genomoncology/biomcp](https://github.com/genomoncology/biomcp) - **Issues**: [Report bugs or request features](https://github.com/genomoncology/biomcp/issues) - **Discussions**: [Ask questions and share tips](https://github.com/genomoncology/biomcp/discussions) ## License BioMCP is licensed under the MIT License. See [LICENSE](https://github.com/genomoncology/biomcp/blob/main/LICENSE) for details.