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BioMCP: Biomedical MCP Server

@genomoncology

代码仓库主页

基本信息

分类

其他

许可证

MIT

传输方式

stdio

作者

genomoncology

关于 BioMCP: Biomedical MCP Server

BioMCP: Biomedical Model Context Protocol

#bioinformatics#ai#genomics#mcp#pubmed#pubmed-central#medical#clinical-trials#llm#model-context-protocol#mcp-server

BioMCP: Biomedical MCP Server 配置

使用下面的配置,将此服务器添加到你的 MCP 客户端。

{
  "mcpServers": {
    "biomcp": {
      "command": "uv",
      "args": [
        "tool",
        "install",
        "biomcp-cli"
      ]
    }
  }
}

BioMCP: Biomedical MCP Server 工具

工具列表暂未提供

当前收录暂时没有可展示的工具列表，不代表服务没有工具。请查阅项目文档了解支持的能力。

工具是从 README 中自动提取的。维护者可以在 ## Tools 标题下列出工具,即可填充这部分内容。

概览

What is BioMCP?

BioMCP is a command-line and MCP server tool that unifies search and retrieval across dozens of biomedical sources (PubTator3, Europe PMC, ClinVar, UniProt, etc.) behind a single grammar. It is designed for researchers, clinicians, and AI agents who need compact, evidence-oriented results without rebuilding workflows for each source.

How to use BioMCP?

Install the biomcp binary via the install script or uv tool install biomcp-cli, then run biomcp serve to start the MCP stdio server. Use commands such as search, get, suggest, enrich, batch, or study directly in the terminal, or register the server with Claude Desktop, Claude Code, or Codex. Optional API keys improve rate limits and unlock additional data.

Key features of BioMCP

  • Search literature across PubTator3, Europe PMC, and Semantic Scholar
  • Pivot between genes, variants, drugs, diseases, and more
  • Route questions to shipped worked examples with suggest
  • Analyze local study datasets with native terminal charts
  • Follow paper trails with citations, references, and recommendations
  • Enrich gene sets via g:Profiler and batch multiple focused queries

Use cases of BioMCP

  • Literature discovery: search articles by gene and disease filters
  • Variant interpretation: get ClinVar, gnomAD, and OncoKB data for a variant
  • Drug interaction scanning: query drugs and their adverse events or approvals
  • Gene-set enrichment: run enrichment analysis on a list of genes
  • Cross-entity pivoting: move from a disease to its known drugs, trials, or articles

常见问题

1

What biomedical sources does BioMCP query?

BioMCP queries over 40 upstream providers including PubTator3, Europe PMC, MyGene.info, UniProt, ClinVar, ClinicalTrials.gov, OpenFDA, MyDisease.info, Reactome, and many more, depending on the entity and command.

2

Do I need API keys to use BioMCP?

Most commands work without credentials. Optional keys such as `NCBI_API_KEY`, `S2_API_KEY`, `OPENFDA_API_KEY`, and `ONCOKB_TOKEN` improve rate limits or unlock additional data sections (e.g., Semantic Scholar TLDRs, OncoKB variant evidence).

3

How do I pivot between different entities?

Use built-in cross-entity helpers like `biomcp variant trials "BRAF V600E"` or `biomcp disease drugs melanoma`. These commands pivot from one entity to related entities without rebuilding filters.

4

What transport protocols does BioMCP support?

BioMCP supports stdio (local MCP server) and HTTP (remote server via `biomcp serve-http`). The HTTP server exposes health probes and a Streamable HTTP MCP endpoint.

5

Are there any known limitations in data coverage?

References and recommendations for articles can be empty for paywalled papers because of publisher elision in Semantic Scholar upstream coverage. Additionally, some detail sections (e.g., diagnostics, funding) remain opt‑in and are not included in the `all` shortcut.

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