kegg-pathway

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# KEGG Pathway Database REST API

Access the Kyoto Encyclopedia of Genes and Genomes (KEGG) for pathway maps, gene
annotations, compound data, drug info, and disease records. No authentication required.

## API Endpoints

Base: `https://rest.kegg.jp`

### GET /list/{database} -- List all entries in a database
```bash
# List all human pathways
curl -s "https://rest.kegg.jp/list/pathway/hsa"

# List all KEGG organisms
curl -s "https://rest.kegg.jp/list/organism"
```

### GET /find/{database}/{query} -- Search by keyword
```bash
# Search pathways for "apoptosis"
curl -s "https://rest.kegg.jp/find/pathway/apoptosis"

# Search genes for BRCA1 across all organisms
curl -s "https://rest.kegg.jp/find/genes/brca1"

# Search compounds by name
curl -s "https://rest.kegg.jp/find/compound/glucose"

# Search diseases by keyword
curl -s "https://rest.kegg.jp/find/disease/diabetes"
```

### GET /get/{entry} -- Retrieve full entry details
```bash
# Get a pathway entry (human apoptosis pathway)
curl -s "https://rest.kegg.jp/get/hsa04210"

# Get a human gene entry
curl -s "https://rest.kegg.jp/get/hsa:7157"

# Get a compound entry (glucose)
curl -s "https://rest.kegg.jp/get/C00031"

# Get a KEGG Orthology entry
curl -s "https://rest.kegg.jp/get/K00001"

# Get pathway map as image
curl -s "https://rest.kegg.jp/get/hsa04210/image" -o apoptosis.png
```

### GET /link/{target}/{source} -- Cross-reference between databases
```bash
# Find all genes in a pathway
curl -s "https://rest.kegg.jp/link/hsa/hsa04210"

# Find pathways associated with a gene
curl -s "https://rest.kegg.jp/link/pathway/hsa:7157"

# Find compounds in a pathway
curl -s "https://rest.kegg.jp/link/compound/hsa00010"

# Find diseases linked to a gene
curl -s "https://rest.kegg.jp/link/disease/hsa:672"

# Link KEGG Orthology to pathways
curl -s "https://rest.kegg.jp/link/pathway/ko:K00001"
```

### GET /conv/{target}/{source} -- Convert between ID systems
```bash
# Convert KEGG gene IDs to NCBI Gene IDs
curl -s "https://rest.kegg.jp/conv/ncbi-geneid/hsa:7157"

# Convert NCBI Gene IDs to KEGG
curl -s "https://rest.kegg.jp/conv/hsa/ncbi-geneid:7157"

# Convert KEGG compound to PubChem
curl -s "https://rest.kegg.jp/conv/pubchem/compound:C00031"

# Convert UniProt to KEGG gene IDs
curl -s "https://rest.kegg.jp/conv/hsa/uniprot:P04637"
```

## Supported Databases

| Database   | Code        | Description                            |
|-----------|-------------|----------------------------------------|
| Pathway   | `pathway`   | Metabolic and signaling pathway maps   |
| Module    | `module`    | Functional units within pathways       |
| KO        | `ko`        | KEGG Orthology (functional orthologs)  |
| Genome    | `genome`    | Organism genomes                       |
| Genes     | `genes`     | Gene entries per organism (e.g., hsa)  |
| Compound  | `compound`  | Small molecules and metabolites        |
| Drug      | `drug`      | Drug and pharmaceutical entries        |
| Disease   | `disease`   | Human disease entries                  |

## Common Patterns

```bash
# Full workflow: find pathways for a gene, then get pathway details
curl -s "https://rest.kegg.jp/link/pathway/hsa:7157"   # Step 1: find pathways
curl -s "https://rest.kegg.jp/get/hsa04115"             # Step 2: get details

# Map between KEGG and external IDs for batch processing
curl -s "https://rest.kegg.jp/conv/ncbi-geneid/hsa"
```

## Organism Codes

Common codes: `hsa` (human), `mmu` (mouse), `rno` (rat), `dme` (fly), `sce` (yeast), `eco` (E. coli).

## Best Practices

1. KEGG returns tab-separated plain text by default -- parse with `cut`, `awk`, or similar.
2. Use `/link` for mapping between databases and `/conv` for external ID conversion.
3. Prefix gene IDs with the organism code (e.g., `hsa:7157` for human TP53).
4. Pathway IDs use organism prefix + number (e.g., `hsa04210`); use `map04210` for reference.
5. No authentication is required, but KEGG limits heavy automated access -- keep requests reasonable.

From beita6969/ScienceClaw, MIT.

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