AGR MCP Server

MCP server for querying Alliance of Genome Resources - genomics data across model organisms.

Installation

Claude Desktop

Add to ~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows):

{
  "mcpServers": {
    "agr-genomics": {
      "command": "npx",
      "args": ["-y", "agr-mcp-server"]
    }
  }
}

Claude Code (CLI)

Add to ~/.claude/settings.json:

{
  "mcpServers": {
    "agr-genomics": {
      "command": "npx",
      "args": ["-y", "agr-mcp-server"]
    }
  }
}

Cursor

Add to Cursor settings (Settings > MCP Servers):

{
  "agr-genomics": {
    "command": "npx",
    "args": ["-y", "agr-mcp-server"]
  }
}

Windsurf

Add to ~/.codeium/windsurf/mcp_config.json:

{
  "mcpServers": {
    "agr-genomics": {
      "command": "npx",
      "args": ["-y", "agr-mcp-server"]
    }
  }
}

From source

git clone https://github.com/nuin/agr-mcp-server-js.git
cd agr-mcp-server-js
npm install && npm run build

Then use the local path in your config:

{
  "mcpServers": {
    "agr-genomics": {
      "command": "node",
      "args": ["/path/to/agr-mcp-server-js/dist/index.js"]
    }
  }
}

Usage

Ask questions naturally:

• "Search for BRCA1 genes in human"
• "What genes are involved in DNA repair?"
• "Get information about HGNC:1100"
• "Find orthologs of insulin gene"
• "What diseases are associated with TP53?"
• "Show me expression data for daf-2 in worm"

Supported Species

Human, mouse, rat, zebrafish, fly, worm, yeast, xenopus

Tools

| Tool | Description | |------|-------------| | search_genes | Search genes with optional species filter | | get_gene_info | Detailed gene information (symbol, location, synonyms) | | get_gene_diseases | Disease associations for a gene | | search_diseases | Search diseases by name | | get_gene_expression | Expression data across tissues/stages | | find_orthologs | Cross-species homologs | | get_gene_phenotypes | Phenotype annotations | | get_gene_interactions | Molecular and genetic interactions | | get_gene_alleles | Alleles/variants for a gene | | search_alleles | Search alleles by name | | get_species_list | List supported model organisms |

Gene ID Formats

| Species | Format | Example | |---------|--------|---------| | Human | HGNC:* | HGNC:1100 | | Mouse | MGI:* | MGI:95892 | | Rat | RGD:* | RGD:3889 | | Zebrafish | ZFIN:ZDB-GENE-* | ZFIN:ZDB-GENE-990415-72 | | Fly | FB:FBgn* | FB:FBgn0000017 | | Worm | WB:WBGene* | WB:WBGene00000898 | | Yeast | SGD:S* | SGD:S000002536 | | Xenopus | Xenbase:XB-GENE-* | Xenbase:XB-GENE-485905 |

Data Sources

• Search & gene data: Alliance of Genome Resources API
• Advanced search: AllianceMine

License

MIT