KEGG Pathway Database Query

Query the KEGG REST API for biological pathways, genes, and compounds.

When to Use

• User asks about biological pathways (glycolysis, apoptosis, etc.)
• User wants to find which pathways a gene is in
• User asks about KEGG pathway IDs
• User wants pathway gene lists

How to Execute

import requests

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

# 1. Find pathways by keyword
def find_pathways(keyword, organism="hsa"):
    url = f"{BASE_URL}/find/pathway/{keyword}"
    r = requests.get(url)
    lines = r.text.strip().split('\n')
    results = []
    for line in lines:
        if line:
            parts = line.split('\t')
            pid = parts[0].replace("map", organism) if organism else parts[0]
            results.append({"id": pid, "name": parts[1] if len(parts) > 1 else ""})
    return results

# 2. Get pathway details
def get_pathway(pathway_id):
    url = f"{BASE_URL}/get/{pathway_id}"
    r = requests.get(url)
    return r.text

# 3. Get genes in a pathway
def get_pathway_genes(pathway_id):
    url = f"{BASE_URL}/link/genes/{pathway_id}"
    r = requests.get(url)
    genes = []
    for line in r.text.strip().split('\n'):
        if line:
            parts = line.split('\t')
            if len(parts) >= 2:
                genes.append(parts[1])
    return genes

# 4. Get gene info
def get_gene(kegg_gene_id):
    url = f"{BASE_URL}/get/{kegg_gene_id}"
    r = requests.get(url)
    return r.text

# 5. Find genes by name
def find_gene(gene_name, organism="hsa"):
    url = f"{BASE_URL}/find/{organism}/{gene_name}"
    r = requests.get(url)
    return r.text

# 6. List all human pathways
def list_pathways(organism="hsa"):
    url = f"{BASE_URL}/list/pathway/{organism}"
    r = requests.get(url)
    return r.text

# Example
pathways = find_pathways("apoptosis")
for p in pathways[:5]:
    print(f"{p['id']}: {p['name']}")

API Pattern

https://rest.kegg.jp/<operation>/<argument>

Operation	Example	Use
list	/list/pathway/hsa	List all human pathways
find	/find/pathway/cancer	Search by keyword
get	/get/hsa:672	Get BRCA1 gene info
link	/link/genes/hsa00010	Get genes in pathway
conv	/conv/genes/ncbi-geneid:672	Convert IDs

Organism Codes

• hsa = Human, mmu = Mouse, rno = Rat, dme = Fly, sce = Yeast, eco = E. coli

Follow-up Suggestions

• "Want me to get the full gene list for this pathway?"
• "Should I visualize which of your genes overlap with this pathway?"
• "Want me to check related pathways?"