biomcp/mkdocs.yml at main · genomoncology/biomcp · GitHub

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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
  - Blog:
      - "We Deleted 35 Tools and Our Agent Got Better": blog/we-deleted-35-tools.md
  - Policies: policies.md
  - Troubleshooting: troubleshooting.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