Genome MCP

基因组MCP

通过模型上下文协议实现人工智能驱动的基因组智能

      

基因组MCP 是研究级 模型上下文协议（MCP）服务器 这使人工智能代理能够查询临床基因组学数据库，检索支持科学文献，分析群体遗传学，并可视化生物途径——所有这些都是实时的。

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🖥️ CLI工具

GenomeMCP包括一个漂亮的命令行界面，具有丰富的格式和交互式TUI模式。

快速安装

# Recommended (any platform with Python)
pipx install genomemcp

# macOS (Homebrew)
brew install nexisdev/tap/genomemcp

# Windows (Scoop)
scoop bucket add genomemcp https://github.com/nexisdev/scoop-genomemcp
scoop install genomemcp

# From source
git clone https://github.com/nexisdev/GenomeMCP.git
cd GenomeMCP && ./install.sh

独立二进制文件 可用的 .

CLI命令

genomemcp search BRCA1              # 🔍 Search ClinVar
genomemcp variant 12345             # 📋 Get variant report
genomemcp gene TP53                 # 🧬 Get gene info
genomemcp pathway EGFR --visualize  # 🔬 Pathway analysis
genomemcp population 1-55516888-G-GA # 👥 gnomAD frequencies
genomemcp discover "Lynch Syndrome" # 🔗 Discover related genes
genomemcp tui                       # 🖥️ Interactive mode

主题选项

genomemcp --theme cyberpunk search BRCA1
genomemcp --theme professional gene TP53
genomemcp --theme minimal pathway EGFR

看 CLI指南 以获取完整的文档。

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🎯 为什么选择GenomeMCP？

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🧬 特性

核心基因组学工具

• search_clinvar(term) --向ClinVar查询基因、变异或疾病
• get_variant_report(id) --详细的临床意义报告
• get_gene_info(symbol) --NCBI基因的基因功能、位置和别名
• get_supporting_literature(id) --PubMed文章链接到变体

群体遗传学

• get_population_stats(variant) --来自gnomAD（基因组聚集数据库）的等位基因频率

通路分析

• get_pathway_info(gene) --基因的反应组生物途径
• visualize_pathway(gene) --生成基因通路关系的Mermaid.js图

发现与合成

• find_related_genes(phenotype) --发现与疾病相关的基因
• get_genomic_context(gene, position) --识别外显子与内含子区域
• get_discovery_evidence(phenotype) --用于人工智能推理的PubMed摘要汇总

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🚀 快速开始

MCP服务器安装

# Clone the repository
git clone https://github.com/nexisdev/GenomeMCP.git
cd GenomeMCP

# Install dependencies with uv
uv sync

# Run the MCP server
uv run python src/main.py

CLI安装

# Using the install script
./install.sh

# Or with pip
pip install genomemcp[cli]

# Or for development
./setup-dev.sh
source .venv/bin/activate

Claude桌面集成

添加到您的 claude_desktop_config.json:

{
  "mcpServers": {
    "genomemcp": {
      "command": "uv",
      "args": [
        "--directory",
        "/path/to/GenomeMCP",
        "run",
        "python",
        "src/main.py"
      ]
    }
  }
}

### ☁️ Cloud Deployment (Railway)

You can deploy the GenomeMCP server to the cloud with one click. It will be exposed as an SSE (Server-Sent Events) endpoint, ready for remote agents.

1. Click the **Deploy on Railway** button above.
2. Provide your `SUPABASE_URL` and `SUPABASE_KEY` (optional, for persistence).
3. Connect your agent to the deployment URL (e.g. `https://your-app.up.railway.app/sse`).

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## 📖 Usage Examples

### Search for a Gene Variant

用户：“哪些变异与BRCA1有关？” 代理使用：search_clinvar（“BRCA1”）

### Get Population Frequency

用户：“变体1-55516888-G-GA有多常见？” 代理使用：get_population_stats（“1-55516888-G-GA”） → 返回gnomAD等位基因频率：0.000123（0.01%）

### Discover Gene-Disease Relationships

用户：“哪些基因与林奇综合征有关？” 试剂用途：查找相关基因（“林奇综合征”） → 返回：MSH2（12个变体）、MLH1（8个变体）和PMS2（5个变体）

### Visualize Pathways

用户：“显示TP53的路径” 代理使用：可视化路径（“TP53”） → 返回美人鱼图：

graph TD TP53((TP53)) TP53 --> P_123["Transcriptional Regulation by TP53"] TP53 --> P_456["Cell Cycle Checkpoints"] TP53 --> P_789["DNA Damage Response"]

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## 🔬 数据源

|来源|说明| API|
| ------------------------------------------------ | -------------------------------- | ------------------------ |
| [克林瓦尔](https://www.ncbi.nlm.nih.gov/clinvar/) |临床变异解释|NCBI电子工具|
| [gnomAD](https://gnomad.broadinstitute.org/) |群体等位基因频率|gnomAD-GraphQL|
| [反应组](https://reactome.org/) |生物途径数据库|反应组内容服务|
| [PubMed](https://pubmed.ncbi.nlm.nih.gov/) |科学文献| NCBI电子公用事业|
| [NCBI基因](https://www.ncbi.nlm.nih.gov/gene/) |基因注释|NCBI电子工具|

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## 🏗️ 建筑

GenomeMCP/ ├── src/ │ ├── main.py # MCP server & tool definitions │ ├── clinvar.py # ClinVar & PubMed API client │ ├── genomics.py # Exon/Intron mapping │ ├── population.py # gnomAD integration │ ├── pathways.py # Reactome integration │ ├── utils.py # Shared utilities │ └── cli/ # Command-line interface │ ├── app.py # Typer CLI application │ ├── formatters/ # Rich output formatters │ ├── tui/ # Textual interactive UI │ └── config.py # Theme configuration ├── tests/ # Unit tests ├── docs/ # Documentation ├── install.sh # Quick install script ├── setup-dev.sh # Development setup └── pyproject.toml # Project configuration

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## 🧪 测试

Run all tests

uv run pytest

Run CLI tests

uv run pytest tests/test_cli.py -v

Run specific test suite

uv run pytest tests/test_phase4.py tests/test_phase5.py

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## 📚 文档

- [CLI指南](docs/cli_guide.md) --命令行界面文档
- [工具参考](docs/tool_reference.md) -完整的API文件
- [架构指南](docs/architecture_and_capabilities.md) --系统设计

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## 🤝 贡献

欢迎投稿！请打开问题或提交拉取请求。

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## 📄 许可证

MIT许可证——见 [许可证](LICENSE) 了解详情。

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## 🔗 关键词

`genomics` `bioinformatics` `clinvar` `gnomad` `mcp` `model-context-protocol` `ai-agent` `claude` `variant-interpretation` `population-genetics` `reactome` `pathway-analysis` `pubmed` `ncbi` `gene-discovery` `clinical-genomics` `precision-medicine` `llm-tools` `cli` `tui` `terminal`

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