Labsco
MCP SERVER

Alliance of Genome Resources (JS)

by nuin ↗

Query genes, diseases, orthologs and expression across the model organisms — and drop into AllianceMine when the fixed lookups run out.

Biomedical: Genomics & Clinical Data
Summary
Alliance data and AllianceMine, from one server.

The API tools cover what you would otherwise click through alliancegenome.org for — what a gene is linked to, its orthologs in mouse, where it is expressed. AllianceMine is the reason to keep it: when the fixed lookups do not answer the question, you can write the query yourself.

What it is

A Node server over the Alliance of Genome Resources. Eleven tools cover the Alliance API — genes, diseases, expression, orthologs, phenotypes, interactions and alleles across human, mouse, rat, zebrafish, fly, worm, yeast and xenopus — and eleven more open AllianceMine, the query engine behind it.

What you get
  • Genes searched with an optional species filter, and one gene read in full — symbol, location, synonyms (`search_genes`, `get_gene_info`)
  • Disease associations for a gene, and disease search by name (`get_gene_diseases`, `search_diseases`)
  • Expression across tissues and stages, phenotype annotations, molecular and genetic interactions (`get_gene_expression`, `get_gene_phenotypes`, `get_gene_interactions`)
  • Cross-species homologs, the alleles and variants recorded for a gene, allele search, and the list of supported organisms (`find_orthologs`, `get_gene_alleles`, `search_alleles`, `get_species_list`)
  • AllianceMine reached three ways — raw PathQuery XML, a JSON query builder with from/select/where, and a natural-language mode that hands the schema back for the model to work from (`mine_query`, `mine_query_builder`, `mine_natural_query`, `mine_search`)
  • Prebuilt AllianceMine templates such as `Gene_Alleles`, `Gene_DOTerm`, `Gene_GOTerms` and `GOTerm_Genes`, listed and run (`mine_list_templates`, `mine_run_template`)
  • Gene and protein lists fetched, created, added to and deleted (`mine_get_lists`, `mine_get_list`, `mine_create_list`, `mine_add_to_list`, `mine_delete_list`)
Requirements

`npx -y agr-mcp-server` in the client config, or a global npm install. No key and no account for the lookups — they run against the Alliance's public API and AllianceMine. Creating, adding to or deleting a list needs an AllianceMine token in `ALLIANCEMINE_TOKEN`. Gene identifiers are the source-native ones and are case-sensitive: `HGNC:1100` for human, `MGI:95892` for mouse, `WB:WBGene00000898` for worm, and so on.

Setup effort

One command — npm install -g agr-mcp-server