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

License

MIT

AGR MCP Server

AGR MCP Server

Installation

Option 1: npx (Recommended)

Option 2: Global install

Config file locations

Usage

Supported Species

Tools

AGR API Tools

AllianceMine Tools

AllianceMine Query Examples

Authentication

Gene ID Formats

Data Sources

License

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