MCP server for Alliance of Genome Resources - access genomics data across model organisms
Agr Js MCP server is a locally run integration for AI assistants that speak the Model Context Protocol. MCP server for Alliance of Genome Resources - access genomics data across model organisms.
Installation goes through your MCP client rather than a global install: point it at agr-mcp-server on npm and it is fetched when the client starts. The copy-paste blocks for Claude Desktop, Claude Code and Cursor are further down this page.
Once Agr Js is connected, these are the calls the assistant has available:
search_genes — Search genes with optional species filterget_gene_info — Detailed gene information (symbol, location, synonyms)get_gene_diseases — Disease associations for a genesearch_diseases — Search diseases by nameget_gene_expression — Expression data across tissues/stagesfind_orthologs — Cross-species homologsget_gene_phenotypes — Phenotype annotationsget_gene_interactions — Molecular and genetic interactionsget_gene_alleles — Alleles/variants for a genesearch_alleles — Search alleles by nameget_species_list — List supported model organismsmine_search — Search AllianceMine for genes, proteins, diseasesYou will need one environment variable: ALLIANCEMINE_TOKEN. The server will not start without them, which is usually why the tools fail to appear on a first run. Keep credentials in your client's env block or a secrets manager rather than in a file you might commit.
This sits in the developer tooling group, where several servers overlap in what they claim to do but differ sharply once you actually set them up. Agr Js's toolset — search_genes, get_gene_info, get_gene_diseases and 11 more — is a fair guide to whether it matches your workflow. It is maintained by nuin; worth a glance at recent repository activity before you build anything load-bearing on it.
This entry was verified against Agr Js's own documentation before publication; SyncDev keeps the directory reviewed rather than auto-generated.
| Tool | What it does |
|---|---|
| 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 |
{
"mcpServers": {
"agr-genomics": {
"command": "npx",
"args": ["-y", "agr-mcp-server"]
}
}
}Configuration as documented by the project. Restart the client after saving.
| Variable | Description | Required |
|---|---|---|
| ALLIANCEMINE_TOKEN | Credential the server authenticates with. | Yes |
Read-only SQL access to Postgres — let your assistant inspect schemas and answer questions from real data.
Manage your whole Supabase project in conversation — database, auth, storage, Edge Functions and branches.
Query, modify and analyse local SQLite databases in conversation — the fastest way to chat with a data file.
Metabase ships its own MCP endpoint — search your BI content, build and run queries, and save questions and dashboards without leaving the chat.
Official MongoDB server covering data, schemas and Atlas management — from find queries to spinning up clusters.
Serverless Postgres with database branching — point your assistant at Neon and let it work on disposable copies.