BioMCP

site_name: BioMCP repo_url: https://github.com/genomoncology/biomcp site_url: https://biomcp.org/ site_description: Biomedical Model Context Protocol Server site_author: Ian Maurer edit_uri: edit/main/docs/ repo_name: genomoncology/biomcp copyright: Maintained by <a href="https://genomoncology.com">genomoncology</a>. nav: - Home: index.md - Getting Started: - Quick Start: getting-started/01-quickstart-cli.md - Claude Desktop: getting-started/02-claude-desktop-integration.md - API Keys: getting-started/03-authentication-and-api-keys.md - FAQ: faq-condensed.md - Troubleshooting: troubleshooting.md - User Guide: - Overview: concepts/01-what-is-biomcp.md - Finding Articles: how-to-guides/01-find-articles-and-cbioportal-data.md - Finding Trials: how-to-guides/02-find-trials-with-nci-and-biothings.md - Analyzing Variants: how-to-guides/03-get-comprehensive-variant-annotations.md - Predicting Effects: how-to-guides/04-predict-variant-effects-with-alphagenome.md - Searching Organizations: how-to-guides/06-search-nci-organizations-and-interventions.md - Research Workflows: workflows/all-workflows.md - Examples: - Pydantic AI Integration: tutorials/pydantic-ai-integration.md - Remote Connection: tutorials/remote-connection.md - BioThings Examples: tutorials/biothings-prompts.md - NCI Examples: tutorials/nci-prompts.md - AlphaGenome Tutorial: tutorials/claude-code-biomcp-alphagenome.md - OpenFDA Examples: tutorials/openfda-prompts.md - Concepts: - Deep Researcher: concepts/02-the-deep-researcher-persona.md - Sequential Thinking: concepts/03-sequential-thinking-with-the-think-tool.md - Reference: - Quick Reference: reference/quick-reference.md - CLI Commands: user-guides/01-command-line-interface.md - MCP Tools: user-guides/02-mcp-tools-reference.md - API Documentation: - API Overview: apis/overview.md - Python SDK: apis/python-sdk.md - Error Codes: apis/error-codes.md - IDE Integration: user-guides/03-integrating-with-ides-and-clients.md - Developer: - Architecture: - Overview: reference/quick-architecture.md - Visual Diagrams: reference/visual-architecture.md - Detailed Diagrams: reference/architecture-diagrams.md - Data Sources: - Overview: backend-services-reference/01-overview.md - PubTator3/PubMed: backend-services-reference/06-pubtator3.md - ClinicalTrials.gov: backend-services-reference/04-clinicaltrials-gov.md - NCI CTS API: backend-services-reference/05-nci-cts-api.md - BioThings Suite: backend-services-reference/02-biothings-suite.md - cBioPortal: backend-services-reference/03-cbioportal.md - AlphaGenome: backend-services-reference/07-alphagenome.md - OpenFDA: tutorials/openfda-integration.md - Development: - Contributing: developer-guides/02-contributing-and-testing.md - Deployment: developer-guides/01-server-deployment.md - BigQuery Monitoring: how-to-guides/05-logging-and-monitoring-with-bigquery.md - Technical Details: - Transport Protocol: developer-guides/04-transport-protocol.md - Error Handling: developer-guides/05-error-handling.md - HTTP Client: developer-guides/06-http-client-and-caching.md - Performance: developer-guides/07-performance-optimizations.md - Third-Party APIs: developer-guides/03-third-party-endpoints.md - Security: - FDA Integration Security: FDA_SECURITY.md - About: - Blog: - Clinical Trial Search: blog/ai-assisted-clinical-trial-search-analysis.md - Researcher Persona: blog/researcher-persona-resource.md - Project: - Changelog: changelog.md - Policies: policies.md - GenomOncology: genomoncology.md plugins: - search: lang: en separator: '[\s\-\.]+' - mkdocstrings: handlers: python: paths: ["src/biomcp"] # Note: sitemap plugin requires additional installation # Uncomment after installing: pip install mkdocs-sitemap # - sitemap: # changefreq: weekly # priority: 0.5 theme: name: material # custom_dir: overrides favicon: assets/favicon.ico logo: assets/icon.png features: - navigation.tabs - navigation.tabs.sticky - navigation.sections - navigation.instant - navigation.tracking - navigation.top - toc.follow - search.suggest - search.highlight palette: - media: "(prefers-color-scheme: light)" scheme: default primary: white accent: deep orange toggle: icon: material/brightness-7 name: Switch to dark mode - 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