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KEGG

Access pathway and biological systems data via the KEGG API.

Overview

KEGG (Kyoto Encyclopedia of Genes and Genomes) provides data on:

  • Pathways - Metabolic and signaling pathways
  • Genes - Organism-specific gene information
  • Compounds - Chemical compounds and reactions
  • Diseases - Disease information and drug targets

Quick Start

from biodbs.fetch import kegg_get, kegg_find, kegg_list, kegg_link

# Get a pathway
pathway = kegg_get("hsa00010")  # Glycolysis

# Find genes
genes = kegg_find("genes", "shiga toxin")

Basic Operations

Get Entry

from biodbs.fetch import kegg_get, kegg_get_batch

# Single entry
entry = kegg_get("hsa:7157")  # TP53 gene
pathway = kegg_get("hsa00010")  # Pathway
compound = kegg_get("C00001")  # Water

# Multiple entries (max 10 per request)
entries = kegg_get_batch(["hsa:7157", "hsa:672", "hsa:675"])

Database Info

from biodbs.fetch import kegg_info

info = kegg_info("pathway")
info = kegg_info("hsa")  # Human genes

List Entries

from biodbs.fetch import kegg_list

# List all human pathways
pathways = kegg_list("pathway", organism="hsa")

# List all compounds
compounds = kegg_list("compound")

from biodbs.fetch import kegg_find

# Search genes
genes = kegg_find("genes", "shiga toxin")

# Search compounds
compounds = kegg_find("compound", "aspirin")

# Search pathways
pathways = kegg_find("pathway", "cancer")

ID Conversion

from biodbs.fetch import kegg_conv

# KEGG to NCBI Gene ID
converted = kegg_conv("ncbi-geneid", ["hsa:7157", "hsa:672"])

# KEGG to UniProt
converted = kegg_conv("uniprot", "hsa:7157")

# Organism-wide conversion
all_human = kegg_conv("ncbi-geneid", "hsa")

Cross-References

from biodbs.fetch import kegg_link

# Genes in a pathway
genes = kegg_link("hsa", "hsa00010")

# Pathways for genes
pathways = kegg_link("pathway", ["hsa:7157", "hsa:672"])

# Compounds in a pathway
compounds = kegg_link("compound", "hsa00010")

Drug-Drug Interactions

from biodbs.fetch import kegg_ddi

# Check drug interactions
interactions = kegg_ddi(["D00001", "D00002"])

Using the Fetcher Class

from biodbs.fetch.KEGG import KEGG_Fetcher

fetcher = KEGG_Fetcher()
pathway = fetcher.get("hsa00010")
  • Reactome - Alternative pathway database with more detailed reaction-level data. Good for complementary analysis.
  • UniProt - Get detailed protein information for KEGG genes using kegg_conv("uniprot", ...).
  • PubChem - Additional chemical information for KEGG compounds.
  • Over-Representation Analysis - Use KEGG pathways for gene set enrichment analysis with ora_kegg().
  • Knowledge Graphs - Build knowledge graphs from KEGG data with build_kegg_graph().