mkdocs.yml

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
      - MCP Clients: getting-started/mcp-clients.md
      - Claude Desktop: getting-started/claude-desktop.md
      - Remote HTTP Server: getting-started/remote-http.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
      - Discover: user-guide/discover.md
      - Gene: user-guide/gene.md
      - Variant: user-guide/variant.md
      - Article: user-guide/article.md
      - Trial: user-guide/trial.md
      - Diagnostic: user-guide/diagnostic.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
  - Sources:
      - Overview: sources/index.md
      - PubMed: sources/pubmed.md
      - ClinicalTrials.gov: sources/clinicaltrials-gov.md
      - ClinVar: sources/clinvar.md
      - OpenFDA: sources/openfda.md
      - UniProt: sources/uniprot.md
      - gnomAD: sources/gnomad.md
      - Reactome: sources/reactome.md
      - Semantic Scholar: sources/semantic-scholar.md
      - ChEMBL: sources/chembl.md
      - OpenTargets: sources/opentargets.md
      - SEER Explorer: sources/seer.md
      - CIViC: sources/civic.md
      - OncoKB: sources/oncokb.md
      - cBioPortal: sources/cbioportal.md
      - DDInter: sources/ddinter.md
      - EMA: sources/ema.md
      - WHO Prequalification: sources/who-prequalification.md
      - NCBI Genetic Testing Registry: sources/gtr.md
      - WHO Prequalified IVD: sources/who-ivd.md
      - CDC CVX/MVX: sources/cdc-cvx.md
      - CDC WONDER VAERS: sources/vaers.md
      - MedlinePlus: sources/medlineplus.md
      - KEGG: sources/kegg.md
      - PharmGKB / CPIC: sources/pharmgkb.md
      - Human Protein Atlas: sources/human-protein-atlas.md
      - Monarch Initiative: sources/monarch-initiative.md
  - How-To:
      - Annotate Variants: how-to/annotate-variants.md
      - Annotate Variant Structure: how-to/annotate-variant-structure.md
      - Cross-Entity Pivots: how-to/cross-entity-pivots.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
      - Search All Workflow: how-to/search-all-workflow.md
      - Skill Authoring: how-to/skill-authoring.md
      - Skill Validation: how-to/skill-validation.md
      - Guide Workflows: how-to/guide-workflows.md
  - Study Charts:
      - Overview: charts/index.md
      - Bar: charts/bar.md
      - Stacked Bar: charts/stacked-bar.md
      - Pie: charts/pie.md
      - Waterfall: charts/waterfall.md
      - Scatter: charts/scatter.md
      - Heatmap: charts/heatmap.md
      - Histogram: charts/histogram.md
      - Density: charts/density.md
      - Box: charts/box.md
      - Violin: charts/violin.md
      - Ridgeline: charts/ridgeline.md
      - Survival: charts/survival.md
  - Reference:
      - Quick Reference: reference/quick-reference.md
      - Data Sources: reference/data-sources.md
      - Source Licensing: reference/source-licensing.md
      - MCP Server: reference/mcp-server.md
      - Error Codes: reference/error-codes.md
      - Benchmarks: reference/benchmarks.md
      - BioASQ Benchmark: reference/bioasq-benchmark.md
      - FAQ: reference/faq.md
      - Configuration: reference/configuration.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
      - Dependencies: reference/dependencies.md
  - Blog:
      - blog/variant-structure-in-commands.md
      - blog/daraxonrasib-six-commands.md
      - blog/kras-g12c-treatment-landscape.md
      - blog/biomcp-charts.md
      - blog/biomcp-kuva-charts.md
      - blog/biomcp-pubmed-articles.md
      - blog/skillbench-biomcp-skills.md
      - blog/cbioportal-study-analytics.md
      - blog/we-deleted-35-tools.md
  - Privacy Policy: policies.md
  - Troubleshooting: troubleshooting.md

plugins:
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      separator: '[\s\-\.]+'

theme:
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extra:
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    - name: twitter:card
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    - name: twitter:description
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    - name: keywords
      content: biomedical, MCP, CLI, genomics, clinical trials, bioinformatics, Rust

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