kegg-api

name

kegg-api

description

Query the KEGG (Kyoto Encyclopedia of Genes and Genomes) REST API for biological pathway, gene, compound, drug, disease, and reaction data. Use when the user wants to (1) look up KEGG database entries such as genes, pathways, compounds, drugs, diseases, enzymes, or reactions, (2) search KEGG by keywords or chemical properties, (3) convert identifiers between KEGG and external databases (NCBI, UniProt, PubChem, ChEBI), (4) find cross-references between KEGG databases, (5) check drug-drug interactions, or (6) retrieve sequences, structures, pathway maps, or other KEGG data.

KEGG REST API

Query biological data from KEGG via https://rest.kegg.jp.

Constraints: Max 3 requests/second. Academic use only.

Quick Reference

Use scripts/kegg_fetch.sh for all API calls:

# Database info
scripts/kegg_fetch.sh info pathway

# List entries
scripts/kegg_fetch.sh list pathway hsa
scripts/kegg_fetch.sh list organism

# Search
scripts/kegg_fetch.sh find compound sugar
scripts/kegg_fetch.sh find compound 300-310 mol_weight

# Retrieve entries (max 10, flat file by default)
scripts/kegg_fetch.sh get hsa:10458 aaseq
scripts/kegg_fetch.sh get C00001

# Convert IDs
scripts/kegg_fetch.sh conv uniprot hsa
scripts/kegg_fetch.sh conv genes ncbi-geneid:948068

# Cross-references
scripts/kegg_fetch.sh link pathway hsa:10458
scripts/kegg_fetch.sh link drug disease

# Drug-drug interactions
scripts/kegg_fetch.sh ddi D00564+D00123

Operations Summary

Operation	Purpose	Pattern
info	Database release info	info <database>
list	List entries	list <database> [org] or list <entries>
find	Search by keyword/property	find <database> <query> [option]
get	Retrieve entry data	get <entries> [option]
conv	Convert identifiers	conv <target> <source>
link	Cross-references	link <target> <source>
ddi	Drug-drug interactions	ddi <entries>

Common Databases

• Organisms: 3/4-letter codes (e.g., hsa = human, eco = E. coli, sce = yeast)
• Pathways: pathway (reference) or with org code (e.g., list pathway hsa)
• Genes: organism-specific (e.g., hsa:10458) or genes (composite)
• Chemicals: compound, glycan, drug, or ligand (composite)
• Functions: ko, enzyme, reaction, rclass, module
• Health: disease, drug, dgroup, network, variant
• External: ncbi-geneid, ncbi-proteinid, uniprot, pubchem, chebi

Entry ID Formats

• Gene: hsa:10458 (org:id)
• Pathway: map00010 (reference) or hsa00010 (organism-specific)
• Compound: C00001
• Drug: D00001
• Disease: H00001
• Enzyme: ec:1.1.1.1
• Reaction: rn:R00001
• KO: ko:K00001
• Multiple entries: join with +

get Options

Option	For	Returns
aaseq	genes	Amino acid FASTA
ntseq	genes	Nucleotide FASTA
mol	compound/glycan/drug	MOL structure
kcf	compound/glycan/drug	KCF structure
image	compound/glycan/drug/pathway	PNG (1 entry only)
kgml	pathway	KEGG XML (1 entry only)
json	pathway	JSON (1 entry only)
(none)	all	Flat file

find Options (compound/drug only)

Option	Description
formula	Chemical formula (partial match, e.g., C7H10O5)
exact_mass	Exact mass, range with - (e.g., 174.05-174.06)
mol_weight	Molecular weight, range with - (e.g., 300-310)

Workflow Examples

Find genes in a pathway

# List human pathways
scripts/kegg_fetch.sh list pathway hsa
# Get genes linked to a pathway
scripts/kegg_fetch.sh link hsa hsa05130
# Get gene details
scripts/kegg_fetch.sh get hsa:10458

Search compound and get structure

scripts/kegg_fetch.sh find compound aspirin
scripts/kegg_fetch.sh get C01405/mol

Convert gene IDs to UniProt

scripts/kegg_fetch.sh conv uniprot hsa:10458+hsa:150

Check drug interactions

scripts/kegg_fetch.sh ddi D00564
scripts/kegg_fetch.sh ddi D00564+D00123

Find diseases related to a drug

scripts/kegg_fetch.sh link disease D00564

For full API details including all database names, identifier formats, and options, see references/api-reference.md.