Skills › Scientific Agent Skills › database-lookup › kegg.md
kegg.md
80 lines · skills/database-lookup/references/kegg.md at 5f2bc03
KEGG REST API
Raw lines 1 to 2Important: KEGG returns tab-delimited text and flat-file format, NOT JSON.
Raw lines 11 to 1213## Key Operations (URL-path-based, no query parameters)
15| URL Pattern | Description |
16|-------------|-------------|
17| `/list/{database}` | List all entries |
18| `/list/{database}/{organism}` | List entries for organism |
19| `/get/{dbentries}` | Get entry data (flat-file) |
20| `/get/{dbentries}/image` | Pathway image (PNG) |
21| `/get/{dbentries}/kgml` | Pathway as KGML XML |
22| `/find/{database}/{query}` | Search by keyword |
23| `/find/{database}/{query}/formula` | Search by molecular formula |
24| `/find/{database}/{value}/exact_mass` | Search by exact mass |
25| `/link/{target_db}/{source_db}` | Find linked entries between databases |
26| `/link/{target_db}/{dbentries}` | Links for specific IDs |
27| `/conv/{target_db}/{dbentries}` | Cross-reference ID conversion |
28| `/ddi/{dbentries}` | Drug-drug interactions |
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 |
30## Database Codes
32| Code | Database | Example ID |
33|------|----------|------------|
34| `pathway` | Pathways | `hsa00010` |
35| `compound` | Compounds | `C00001` |
36| `drug` | Drugs | `D00001` |
37| `enzyme` | Enzymes | `ec:1.1.1.1` |
38| `genes`/`hsa` | Genes | `hsa:10458` |
39| `disease` | Diseases | `H00001` |
40| `reaction` | Reactions | `R00001` |
41| `ko` | KO orthologs | `K00001` |
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 |
43## Example Calls
45```
46# List human pathways
47https://rest.kegg.jp/list/pathway/hsa
49# Get pathway entry
50https://rest.kegg.jp/get/hsa00010
52# Search compounds by name
53https://rest.kegg.jp/find/compound/aspirin
55# Search by molecular formula
56https://rest.kegg.jp/find/compound/C9H8O4/formula
58# Find pathways for a gene
59https://rest.kegg.jp/link/pathway/hsa:10458
61# Find diseases for a gene
62https://rest.kegg.jp/link/disease/hsa:672
64# Convert KEGG to PubChem IDs
65https://rest.kegg.jp/conv/pubchem/C00001
67# Get multiple entries (max 10, joined with +)
68https://rest.kegg.jp/get/C00001+C00002+C00003
70# Drug-drug interactions
71https://rest.kegg.jp/ddi/D00564+D00110
72```
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+D0011074## Response Format
75Tab-delimited text for list/find/link/conv. Flat-file text for get. **No JSON support.**
Response Format
Tab-delimited text for list/find/link/conv. Flat-file text for get. No JSON support.
Raw lines 74 to 7677## Rate Limits
78KEGG requests at most 3 calls per second; pace below that and honor failures. Batch up to 10 IDs per `/get` with `+`. May return HTTP 403 if too many requests.
80KEGG `conv/pubchem/...` maps to PubChem **Substance IDs (SIDs)**, not Compound IDs (CIDs). Resolve SID to CID through PubChem before joining compound properties. Official contract: https://www.kegg.jp/kegg/rest/keggapi.html
Rate Limits
KEGG requests at most 3 calls per second; pace below that and honor failures. Batch up to 10 IDs per /get with +. May return HTTP 403 if too many requests.
KEGG conv/pubchem/... maps to PubChem Substance IDs (SIDs), not Compound IDs (CIDs). Resolve SID to CID through PubChem before joining compound properties. Official contract: https://www.kegg.jp/kegg/rest/keggapi.html