KEGG Database — Biological Pathway & Molecular Network Queries

KEGG Database — Biological Pathway & Molecular Network Queries

Overview

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a comprehensive bioinformatics resource for biological pathway analysis, molecular interaction networks, and cross-database ID conversion. Access is via a direct REST API with no authentication — all operations use simple HTTP GET requests returning tab-delimited text.

When to Use

• Mapping genes to biological pathways (e.g., "which pathways involve TP53?")
• Retrieving metabolic pathway details, gene lists, or compound structures
• Converting identifiers between KEGG, NCBI Gene, UniProt, and PubChem
• Checking drug-drug interactions from KEGG's pharmacological database
• Building pathway enrichment context (all genes per pathway for an organism)
• Cross-referencing compounds, reactions, enzymes, and pathways
• For Python-native multi-database queries (KEGG + UniProt + Ensembl in one script), prefer bioservices instead
• For pathway visualization, use KEGG Mapper (https://www.kegg.jp/kegg/mapper/) directly

Prerequisites

pip install requests

API constraints:

• Academic use only — commercial use requires a separate KEGG license
• Max 10 entries per get/list/conv/link/ddi call (image/kgml/json: 1 entry only)
• No explicit rate limit, but add time.sleep(0.5) between batch requests to avoid server-side throttling
• Base URL: https://rest.kegg.jp/

Quick Start

import requests
import time

BASE = "https://rest.kegg.jp"

def kegg_get(operation, *args):
    """Generic KEGG REST API caller."""
    url = f"{BASE}/{operation}/{'/'.join(args)}"