How do I install the agr js mcp server?

Use a recorded configuration for your client, replace example credential values and paths, and verify the documented runtime. Restart or reconnect the client, then inspect the available tools.

What credentials does it need?

It reads `ALLIANCEMINE_TOKEN` from the environment. Store these in your client's env block or a secrets manager — never commit them to a repository — and grant the narrowest scope that still covers your use case.

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Agr Js MCP Server

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

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What is the Agr Js MCP Server?

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

More MCP options

Compare MCP servers by category, or browse hosted MCP servers if you prefer an endpoint over a local process.

Maintainer setup documentation.

Recorded tools

Check the linked publisher documentation and your connected client's tool list. Names and availability can vary with the server version and account permissions.

Tool	What it does
from	Gene
select	primaryIdentifier, symbol, name
where	organism.shortName = "H. sapiens", symbol CONTAINS "BRCA"
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
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)

How to install the Agr Js MCP Server

{
  "mcpServers": {
    "agr-genomics": {
      "command": "npx",
      "args": [
        "-y",
        "agr-mcp-server"
      ]
    }
  }
}

From the project documentation. Replace placeholders and example paths before connecting.

Example prompts to try

“Use Agr Js to search genes.”
“Use Agr Js to get gene info.”
“Use Agr Js to get gene diseases.”

Frequently asked questions

MCP server for Alliance of Genome Resources - access genomics data across model organisms Confirm the tools offered by your installed version in the connected client. Tool availability and permissions depend on the server and account configuration.