drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/kegg.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
KEGG REST API		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/kegg.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

KEGG REST API

Base URL

https://rest.kegg.jp

Auth

No API key required. Free for academic use. Commercial use requires license.

Important: KEGG returns tab-delimited text and flat-file format, NOT JSON.

Key Operations (URL-path-based, no query parameters)

URL Pattern	Description
/list/{database}	List all entries
/list/{database}/{organism}	List entries for organism
/get/{dbentries}	Get entry data (flat-file)
/get/{dbentries}/image	Pathway image (PNG)
/get/{dbentries}/kgml	Pathway as KGML XML
/find/{database}/{query}	Search by keyword
/find/{database}/{query}/formula	Search by molecular formula
/find/{database}/{value}/exact_mass	Search by exact mass
/link/{target_db}/{source_db}	Find linked entries between databases
/link/{target_db}/{dbentries}	Links for specific IDs
/conv/{target_db}/{dbentries}	Cross-reference ID conversion
/ddi/{dbentries}	Drug-drug interactions

Database Codes

Code	Database	Example ID
pathway	Pathways	hsa00010
compound	Compounds	C00001
drug	Drugs	D00001
enzyme	Enzymes	ec:1.1.1.1
genes/hsa	Genes	hsa:10458
disease	Diseases	H00001
reaction	Reactions	R00001
ko	KO orthologs	K00001

Example Calls

# List human pathways
https://rest.kegg.jp/list/pathway/hsa

# Get pathway entry
https://rest.kegg.jp/get/hsa00010

# Search compounds by name
https://rest.kegg.jp/find/compound/aspirin

# Search by molecular formula
https://rest.kegg.jp/find/compound/C9H8O4/formula

# Find pathways for a gene
https://rest.kegg.jp/link/pathway/hsa:10458

# Find diseases for a gene
https://rest.kegg.jp/link/disease/hsa:672

# Convert KEGG to PubChem IDs
https://rest.kegg.jp/conv/pubchem/C00001

# Get multiple entries (max 10, joined with +)
https://rest.kegg.jp/get/C00001+C00002+C00003

# Drug-drug interactions
https://rest.kegg.jp/ddi/D00564+D00110

Response Format

Tab-delimited text for list/find/link/conv. Flat-file text for get. No JSON support.

Rate Limits

No published limits. Keep to a few requests per second. Batch up to 10 IDs per /get with +. May return HTTP 403 if too many requests.