kegg-mcp-server
MCP server for the KEGG bioinformatics database REST API
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kegg-mcp-server-python
An unofficial Python Model Context Protocol (MCP) server for the KEGG bioinformatics database. It exposes 33 tools, 8 resource templates, and 3 guided prompts to any MCP-compatible client (Claude Desktop, Claude Code, Cursor, etc.).
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.
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
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.
What's included
33 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) |
8 Resource Templates
Direct URI-based access to KEGG entities:
kegg://pathway/{pathway_id} e.g. kegg://pathway/hsa00010
kegg://gene/{gene_id} e.g. kegg://gene/hsa:1956
kegg://compound/{compound_id} e.g. kegg://compound/C00002
kegg://reaction/{reaction_id} e.g. kegg://reaction/R00756
kegg://disease/{disease_id} e.g. kegg://disease/H00004
kegg://drug/{drug_id} e.g. kegg://drug/D00001
kegg://organism/{org_code} e.g. kegg://organism/hsa
kegg://search/{database}/{query} e.g. kegg://search/compound/glucose
3 Guided Prompts
| Prompt | Arguments | What it does |
|---|---|---|
pathway_enrichment_analysis | gene_list, organism | Maps a gene list to KEGG IDs, aggregates pathway associations, identifies enriched pathways |
drug_target_investigation | drug_name | Drug lookup, target identification, pathway mapping, DDI screening |
metabolic_pathway_comparison | pathway_id, organisms | Compares gene/compound content of a pathway across species |
Transport options
# stdio (default -- for Claude Desktop, Claude Code, uvx)
kegg-mcp-server
# Streamable HTTP (for web/API deployment)
kegg-mcp-server --transport streamable-http --host 0.0.0.0 --port 8080
# python -m also works
python -m kegg_mcp_server
Development
git clone https://github.com/Lucas-Servi/kegg-mcp-server-python
cd kegg-mcp-server-python
pip install -e ".[dev]"
# Run tests
pytest tests/ -v
# Lint
ruff check src/ tests/
# Debug with MCP Inspector
mcp dev kegg-mcp-server
Project structure
src/kegg_mcp_server/
server.py FastMCP instance, lifespan (httpx client + TTL cache), CLI
client.py KEGGClient: async KEGG REST with retry/backoff + KEGG-politeness semaphore
cache.py Per-op TTL cache (info 24h, list 1h, entry ops 5min)
parsers.py KEGG flat-file and tab-delimited response parsers + summarize_flat_entry
errors.py KEGGAPIError exception type
logging.py JSON stderr logger (stdout is reserved for MCP stdio framing)
resources.py 8 MCP resource templates
prompts.py 3 bioinformatics workflow prompts
models/ Pydantic models for all KEGG entity types + EntrySummary + ErrorResult
tools/ 13 tool modules, each with a register(mcp) function; _common.py has the
@kegg_tool error-boundary decorator and shared READ_ONLY annotations
Author
Developed by Lucas Servi (lucasservi@gmail.com) at Elytron Biotech using Claude Code.
Acknowledgments
- Based on Augmented-Nature/KEGG-MCP-Server -- the original TypeScript implementation that served as the foundation for this Python rewrite
- KEGG -- Kyoto Encyclopedia of Genes and Genomes (Kanehisa Laboratories)
- Model Context Protocol -- Anthropic's open protocol for LLM tool use
License
MIT -- see LICENSE.
