kegg-database

# 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 ```bash 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 ```python import requests imp...