KEGG MCP Server

kegg-mcp-server-python

An unofficial Python Model Context Protocol (MCP) server for the KEGG bioinformatics database. It exposes 34 tools, 9 resource templates, and 4 guided prompts to any MCP-compatible client (Claude Desktop, Claude Code, Cursor, etc.). Developed by Elytron Biotech.

Built with FastMCP, returns structured Pydantic JSON (not raw text), and includes per-operation TTL caching, request retry with exponential backoff, KEGG-friendly concurrency limits, structured JSON stderr logging, and batch helpers out of the box. No API key required -- uses the free KEGG REST API.

Responses are token-aware by default: get_*_info tools return a compact EntrySummary (entry id, name, class, description, counts of linked entities) unless you pass detail_level="full". Errors are returned as a typed ErrorResult the model can reason about, not raised as exceptions.

Note: This is a community non-official project and is not affiliated with or endorsed by KEGG or Kanehisa Laboratories.

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Quick start

With uvx (no install)

uvx kegg-mcp-server

With pip

pip install kegg-mcp-server
kegg-mcp-server

Claude Desktop

Add to your claude_desktop_config.json:

{
  "mcpServers": {
    "kegg": {
      "command": "uvx",
      "args": ["kegg-mcp-server"]
    }
  }
}

Config file locations

OS	Path
macOS	~/Library/Application Support/Claude/claude_desktop_config.json
Windows	%APPDATA%\Claude\claude_desktop_config.json
Linux	~/.config/Claude/claude_desktop_config.json

Claude Code

claude mcp add kegg-mcp-server -- uvx kegg-mcp-server

Or install as a plugin (includes slash commands, agent, and skill):

claude plugin install Lucas-Servi/kegg-mcp-server-python

The plugin bundles:

Type	Name	Description
Command	/kegg <query>	Quick search across all KEGG databases
Command	/kegg-pathway <id>	Pathway deep-dive with ASCII visualization
Command	/kegg-drug <name>	Drug targets, pathways, and interactions
Agent	kegg-bioinformatics	Auto-invoked for biological pathway/gene/drug questions
Skill	kegg-analysis	Multi-step workflow guide (enrichment, comparison, investigation)

MCPB bundle (Claude Desktop, no Python required)

Download the latest .mcpb from the releases page and drag it onto Claude Desktop. The bundle vendors all Python dependencies and runs with Claude Desktop's embedded Python.

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What's included

34 Tools

Category	Tools	Examples
Database	get_database_info, list_organisms	Get KEGG release stats, list all ~26k organisms
Pathways	search_pathways, get_pathway_info, get_pathway_genes, get_pathway_compounds, get_pathway_reactions	Search by keyword, get full pathway details
Genes	search_genes, get_gene_info, get_gene_orthologs	Find genes in any organism, cross-species orthologs
Compounds	search_compounds, get_compound_info, get_compound_reactions	Search by name/formula/mass, find reactions
Reactions	search_reactions, get_reaction_info	Equation, enzymes, pathways for any reaction
Enzymes	search_enzymes, get_enzyme_info	EC number lookup, substrates, genes
Diseases	search_diseases, get_disease_info	Disease genes, drugs, pathways
Drugs	search_drugs, get_drug_info, get_drug_interactions	Drug targets, DDI screening
Modules	search_modules, get_module_info	Functional module definitions
Orthology	search_ko_entries, get_ko_info	KEGG Orthology entries
Glycans	search_glycans, get_glycan_info	Glycan composition, reactions
BRITE	search_brite, get_brite_info	Functional hierarchies
Cross-database	batch_entry_lookup, convert_identifiers, find_related_entries	Bulk fetch (up to 50), ID mapping (UniProt, NCBI, ChEBI, PubChem)
Visualization	render_pathway_ascii	ASCII art rendering of pathway topology (chain or grid mode)

9 Resource Templates

Direct URI-based access to KEGG entities: