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AGR MCP Server

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Remote

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

Related MCP server: STRING MCP Server

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

Install Server
A
license - permissive license
B
quality
C
maintenance

How are these scores calculated?

Maintenance

–Maintainers
–Response time
–Release cycle
–Releases (12mo)
Commit activity

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Tools

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