query-kegg

Research

Query KEGG for biological pathways and gene info. Use when user asks about metabolic pathways, signaling pathways, pathway genes, or KEGG IDs. Triggers on "kegg", "pathway", "metabolic pathway", "signaling pathway", "pathway genes".

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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?"