| 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:
scripts/kegg_fetch.sh info pathway
scripts/kegg_fetch.sh list pathway hsa
scripts/kegg_fetch.sh list organism
scripts/kegg_fetch.sh find compound sugar
scripts/kegg_fetch.sh find compound 300-310 mol_weight
scripts/kegg_fetch.sh get hsa:10458 aaseq
scripts/kegg_fetch.sh get C00001
scripts/kegg_fetch.sh conv uniprot hsa
scripts/kegg_fetch.sh conv genes ncbi-geneid:948068
scripts/kegg_fetch.sh link pathway hsa:10458
scripts/kegg_fetch.sh link drug disease
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
scripts/kegg_fetch.sh list pathway hsa
scripts/kegg_fetch.sh link hsa hsa05130
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.
