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"
• "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

Tools

AGR API 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

AllianceMine Tools

Tool	Description
mine_search	Search AllianceMine for genes, proteins, diseases
mine_query	Run raw PathQuery XML queries
mine_query_builder	Build queries using JSON DSL
mine_natural_query	Natural language query (returns schema for LLM)
mine_list_templates	List available query templates
mine_run_template	Run a pre-built query template
mine_get_lists	Get available gene/protein lists
mine_get_list	Get contents of a specific list
mine_create_list	Create a new list (requires auth)
mine_add_to_list	Add items to a list (requires auth)
mine_delete_list	Delete a list (requires auth)

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

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

• Alliance of Genome Resources API
• AllianceMine

License

MIT