AGR MCP Server

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

Tools

AGR API Tools

AllianceMine Tools

AllianceMine Query Examples

Using query builder:

Find human genes with BRCA in symbol:
- from: Gene
- select: primaryIdentifier, symbol, name
- where: organism.shortName = "H. sapiens", symbol CONTAINS "BRCA"

Using templates:

Gene_Alleles - Find alleles for a gene
Gene_DOTerm - Disease annotations for a gene
Gene_GOTerms - GO annotations for a gene
GOTerm_Genes - Find genes by GO term

Authentication

List management operations (mine_create_list, mine_add_to_list, mine_delete_list) require an AllianceMine API token:

{
  "mcpServers": {
    "agr-genomics": {
      "command": "npx",
      "args": ["-y", "agr-mcp-server"],
      "env": {
        "ALLIANCEMINE_TOKEN": "your-token-here"
      }
    }
  }
}

Gene ID Formats

Data Sources

• Alliance of Genome Resources API
• AllianceMine

Installation

Option 1: npx (Recommended)

No installation required. Add to your MCP client config:

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

Option 2: Global install

npm install -g agr-mcp-server

Then use in your config:

{
  "mcpServers": {
    "agr-genomics": {
      "command": "agr-mcp-server"
    }
  }
}

Config file locations

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"
• "Find all human genes with kinase activity"
• "Query AllianceMine for mouse genes on chromosome 11"

Supported Species

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

License

MIT