kegg-mcp

An MCP server that exposes the KEGG REST API — pathways, genes, compounds, reactions, enzymes, diseases, drugs, modules, orthology, glycans, and BRITE hierarchies, with cross-database linking. 34 tools, 8 resource templates, runs over stdio.

Install

npm install -g kegg-mcp

…or run it once with no install:

npx -y kegg-mcp

Requires Node.js ≥ 20.

Connect your MCP client

Add a kegg server to your client config (Claude Desktop, Cursor, VS Code, Cline, …):

{
  "mcpServers": {
    "kegg": {
      "command": "npx",
      "args": ["-y", "kegg-mcp"]
    }
  }
}

Prefer a global install? Use "command": "kegg-mcp" with no args.

Highlights

• 34 tools across every major KEGG database
• 8 resource templates (kegg://pathway/{id}, kegg://gene/{org}:{id}, …)
• Polite rate limiting (≤ 3 req/s), retries with exponential backoff, 30 s timeouts, keep-alive
• Native fetch — zero runtime deps beyond the MCP SDK
• TypeScript, unit tests with real KEGG fixtures, live integration tests, CI on Node 20/22/24

Quick examples

search_pathways(query="glycolysis")
get_pathway_info(pathway_id="hsa00010")
get_pathway_genes(pathway_id="hsa00010")
search_genes(query="insulin", organism_code="hsa")
get_gene_info(gene_id="hsa:3630", include_sequences=true)
search_compounds(query="glucose")
get_compound_info(compound_id="C00031")
convert_identifiers(source_db="hsa", target_db="ncbi-geneid")
batch_entry_lookup(entries=["hsa:3630", "hsa:3631"])
kegg_health_check()

Tools (34)

Info — get_database_info, list_organisms Pathways — search_pathways, get_pathway_info, get_pathway_genes, get_pathway_compounds, get_pathway_reactions Genes — search_genes, get_gene_info, get_gene_orthologs Compounds — search_compounds, get_compound_info, get_compound_reactions Reactions & enzymes — search_reactions, get_reaction_info, search_enzymes, get_enzyme_info Disease & drugs — search_diseases, get_disease_info, search_drugs, get_drug_info, get_drug_interactions Modules & orthology — search_modules, get_module_info, search_ko_entries, get_ko_info Glycans & BRITE — search_glycans, get_glycan_info, search_brite, get_brite_info Cross-db & batch — convert_identifiers, find_related_entries, batch_entry_lookup Health — kegg_health_check

Resource templates (8)

kegg://pathway/{pathway_id} · kegg://gene/{org}:{gene_id} · kegg://compound/{compound_id} · kegg://reaction/{reaction_id} · kegg://disease/{disease_id} · kegg://drug/{drug_id} · kegg://organism/{org_code} · kegg://search/{database}/{query}

Develop

git clone https://github.com/AriaShishegaran/kegg-mcp.git
cd kegg-mcp
npm install
npm run build              # outputs to dist/
npm test                   # unit tests
npm run test:integration   # live tests against rest.kegg.jp

Script	What it does
npm run build	Compile to dist/
npm run typecheck	Type-check only
npm run lint	ESLint
npm test	Unit tests
npm run test:integration	Live tests against rest.kegg.jp
npm start	Run the server

Releases are automated via release-please from Conventional Commits. See CONTRIBUTING.md.

KEGG API terms

rest.kegg.jp is academic use only. Commercial use requires a license from Kanehisa Laboratories.

License

MIT © Aria