AGR MCP Server

AGR MCP Server

Enables querying genomics data from the Alliance of Genome Resources across model organisms including human, mouse, rat, zebrafish, fly, worm, yeast, and xenopus. Supports gene searches, disease associations, expression data, orthologs, phenotypes, and molecular interactions through natural language.

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AGR MCP Server

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

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

Client Config path
Claude Desktop (macOS) ~/Library/Application Support/Claude/claude_desktop_config.json
Claude Desktop (Windows) %APPDATA%\Claude\claude_desktop_config.json
Claude Code ~/.claude/settings.json
Cursor Settings > MCP Servers
Windsurf ~/.codeium/windsurf/mcp_config.json

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

License

MIT

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