Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@AGR MCP Serversearch for TP53 gene in human and show disease associations"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
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-serverThen use in your config:
{
"mcpServers": {
"agr-genomics": {
"command": "agr-mcp-server"
}
}
}Config file locations
Client | Config path |
Claude Desktop (macOS) |
|
Claude Desktop (Windows) |
|
Claude Code |
|
Cursor | Settings > MCP Servers |
Windsurf |
|
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 with optional species filter |
| Detailed gene information (symbol, location, synonyms) |
| Disease associations for a gene |
| Search diseases by name |
| Expression data across tissues/stages |
| Cross-species homologs |
| Phenotype annotations |
| Molecular and genetic interactions |
| Alleles/variants for a gene |
| Search alleles by name |
| List supported model organisms |
AllianceMine Tools
Tool | Description |
| Search AllianceMine for genes, proteins, diseases |
| Run raw PathQuery XML queries |
| Build queries using JSON DSL |
| Natural language query (returns schema for LLM) |
| List available query templates |
| Run a pre-built query template |
| Get available gene/protein lists |
| Get contents of a specific list |
| Create a new list (requires auth) |
| Add items to a list (requires auth) |
| 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 termAuthentication
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 |
|
|
Mouse |
|
|
Rat |
|
|
Zebrafish |
|
|
Fly |
|
|
Worm |
|
|
Yeast |
|
|
Xenopus |
|
|
Data Sources
License
MIT
Resources
Unclaimed servers have limited discoverability.
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If you are the server author, to access and configure the admin panel.