BioMCP

# Quickstart: BioMCP CLI Get started with BioMCP in under 5 minutes! This guide walks you through installation and your first biomedical search. ## Prerequisites - Python 3.10 or higher - [uv](https://docs.astral.sh/uv/) package manager (recommended) or pip ## Installation ### Option 1: Using uv (Recommended) ```bash # Install uv if you haven't already curl -LsSf https://astral.sh/uv/install.sh | sh # Install BioMCP uv tool install biomcp ``` ### Option 2: Using pip ```bash pip install biomcp ``` ## Your First Search Let's search for recent articles about BRAF mutations in melanoma: ```bash biomcp article search \ --gene BRAF --disease melanoma --limit 5 ``` This command: - Searches PubMed/PubTator3 for articles - Filters by BRAF gene and melanoma disease - Returns the 5 most recent results - Automatically includes cBioPortal cancer genomics data - Includes preprints from bioRxiv/medRxiv by default ## Understanding the Output The search returns: 1. **cBioPortal Summary** (if gene specified): Cancer genomics data showing mutation frequencies and hotspots 2. **Article Results**: Each result includes: - Title and authors - Journal and publication date - PubMed ID and direct link - Abstract snippet - Annotated entities (genes, diseases, chemicals) ## Essential Commands ### Search Clinical Trials Find active trials for lung cancer: ```bash biomcp trial search \ --condition "lung cancer" \ --status RECRUITING --limit 5 ``` ### Get Gene Information Retrieve details about the TP53 tumor suppressor: ```bash biomcp gene get TP53 ``` ### Look Up Drug Information Get details about imatinib (Gleevec): ```bash biomcp drug get imatinib ``` ### Search for Genetic Variants Find pathogenic variants in the BRCA1 gene: ```bash biomcp variant search \ --gene BRCA1 --significance pathogenic \ --limit 5 ``` ## Next Steps ### Set Up API Keys (Optional but Recommended) Some features require API keys for enhanced functionality: ```bash # For NCI clinical trials database export NCI_API_KEY="your-key-here" # For AlphaGenome variant predictions export ALPHAGENOME_API_KEY="your-key-here" # For additional cBioPortal features export CBIO_TOKEN="your-token-here" ``` See [Authentication and API Keys](03-authentication-and-api-keys.md) for detailed setup. ### Explore Advanced Features - **Combine Multiple Filters**: ```bash biomcp article search \ --gene EGFR --disease "lung cancer" \ --chemical erlotinib ``` - **Use OR Logic in Keywords**: ```bash biomcp article search --gene BRAF --keyword "V600E|p.V600E|c.1799T>A" ``` - **Exclude Preprints**: ```bash biomcp article search --gene TP53 --no-preprints ``` ### Get Help View all available commands: ```bash biomcp --help ``` Get help for a specific command: ```bash biomcp article search --help ``` ## Common Use Cases ### 1. Research a Specific Mutation ```bash # Find articles about EGFR T790M resistance mutation biomcp article search --gene EGFR \ --keyword "T790M|p.T790M" \ --disease "lung cancer" ``` ### 2. Find Trials for a Patient ```bash # Active trials for HER2-positive breast cancer biomcp trial search \ --condition "breast cancer" \ --keyword "HER2 positive" \ --status RECRUITING ``` ### 3. Investigate Drug Mechanisms ```bash # Get information about pembrolizumab biomcp drug get pembrolizumab # Find articles about its use in melanoma biomcp article search --chemical pembrolizumab --disease melanoma ``` ## Troubleshooting ### Command Not Found If `biomcp` is not recognized: - Ensure your PATH includes the installation directory - Try running with full path: `~/.local/bin/biomcp` - Restart your terminal after installation ### No Results Found If searches return no results: - Check spelling of gene names (use official symbols) - Try broader search terms - Remove filters one by one to identify the constraint ### API Rate Limits If you encounter rate limit errors: - Add delays between requests - Consider setting up API keys for higher limits - Use the `--limit` parameter to reduce result count ## Next Steps Now that you've run your first searches, explore these resources: 1. **[Complete CLI Reference](../user-guides/01-command-line-interface.md)** - Comprehensive documentation for all commands and options 2. **[Claude Desktop Integration](02-claude-desktop-integration.md)** - Use BioMCP with AI assistants 3. **[Set up API Keys](03-authentication-and-api-keys.md)** - Enable advanced features with NCI, AlphaGenome, and cBioPortal 4. **[How-to Guides](../how-to-guides/01-find-articles-and-cbioportal-data.md)** - Step-by-step tutorials for complex research workflows 5. **[Deep Researcher Persona](../concepts/02-the-deep-researcher-persona.md)** - Learn about BioMCP's philosophy and methodology Happy researching! 🧬🔬