site_name: BioMCP
repo_url: https://github.com/genomoncology/biomcp
site_url: https://biomcp.org/
site_description: Single-binary CLI and MCP server for querying biomedical databases
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:
- Installation: getting-started/installation.md
- First Query: getting-started/first-query.md
- Claude Desktop: getting-started/claude-desktop.md
- API Keys: getting-started/api-keys.md
- Skills: getting-started/skills.md
- Concepts:
- What is BioMCP?: concepts/what-is-biomcp.md
- Progressive Disclosure: concepts/progressive-disclosure.md
- User Guide:
- CLI Reference: user-guide/cli-reference.md
- Gene: user-guide/gene.md
- Variant: user-guide/variant.md
- Article: user-guide/article.md
- Trial: user-guide/trial.md
- Drug: user-guide/drug.md
- Disease: user-guide/disease.md
- Pathway: user-guide/pathway.md
- Protein: user-guide/protein.md
- Adverse Event: user-guide/adverse-event.md
- PGx: user-guide/pgx.md
- GWAS: user-guide/gwas.md
- Phenotype: user-guide/phenotype.md
- How-To:
- Annotate Variants: how-to/annotate-variants.md
- Find Articles: how-to/find-articles.md
- Find Trials: how-to/find-trials.md
- Predict Effects: how-to/predict-effects.md
- Reproduce Papers: how-to/reproduce-papers.md
- Skill Validation: how-to/skill-validation.md
- Reference:
- Quick Reference: reference/quick-reference.md
- Data Sources: reference/data-sources.md
- MCP Server: reference/mcp-server.md
- Error Codes: reference/error-codes.md
- Benchmarks: reference/benchmarks.md
- FAQ: reference/faq.md
- Source Versioning: reference/source-versioning.md
- Article Keyword Search: reference/article-keyword-search.md
- CIViC Sections: reference/civic-sections.md
- Drug Approvals & AE Summary: reference/drug-approvals-and-ae-summary.md
- Policies: policies.md
- Troubleshooting: troubleshooting.md
- Changelog: changelog.md
plugins:
- search:
lang: en
separator: '[\s\-\.]+'
theme:
name: material
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
- content.code.copy
palette:
- media: "(prefers-color-scheme: light)"
scheme: default
primary: white
accent: deep orange
toggle:
icon: material/brightness-7
name: Switch to dark mode
- media: "(prefers-color-scheme: dark)"
scheme: slate
primary: black
accent: deep orange
toggle:
icon: material/brightness-4
name: Switch to light mode
icon:
repo: fontawesome/brands/github
extra:
social:
- icon: fontawesome/brands/github
link: https://github.com/genomoncology/biomcp
meta:
- property: og:type
content: website
- property: og:title
content: BioMCP - Biomedical CLI and MCP Server
- property: og:description
content: Single-binary CLI and MCP server for querying 15 biomedical databases
- property: og:image
content: https://biomcp.org/assets/icon.png
- property: og:url
content: https://biomcp.org/
- name: twitter:card
content: summary
- name: twitter:title
content: BioMCP - Biomedical CLI and MCP Server
- name: twitter:description
content: Single-binary CLI and MCP server for querying 15 biomedical databases
- name: keywords
content: biomedical, MCP, CLI, genomics, clinical trials, bioinformatics, Rust
extra_css:
- stylesheets/extra.css
markdown_extensions:
- toc:
permalink: true
- admonition
- pymdownx.details
- pymdownx.highlight:
anchor_linenums: true
- pymdownx.inlinehilite
- pymdownx.snippets
- pymdownx.superfences
- pymdownx.tabbed:
alternate_style: true
- tables
