Query Reactome Agent Skill

import requests
import json

CONTENT_URL = "https://reactome.org/ContentService"
ANALYSIS_URL = "https://reactome.org/AnalysisService"

# 1. Search pathways by keyword
def search_pathways(keyword, species="Homo sapiens"):
    url = f"{CONTENT_URL}/search/query"
    params = {"query": keyword, "species": species, "types": "Pathway", "cluster": True}
    r = requests.get(url, params=params)
    r.raise_for_status()
    return r.json()

# 2. Get pathway details
def get_pathway(pathway_id):
    url = f"{CONTENT_URL}/data/query/{pathway_id}"
    r = requests.get(url, headers={"Accept": "application/json"})
    r.raise_for_status()
    return r.json()

# 3. Get genes/proteins in a pathway
def get_pathway_participants(pathway_id):
    url = f"{CONTENT_URL}/data/participants/{pathway_id}"
    r = requests.get(url, headers={"Accept": "application/json"})
    r.raise_for_status()
    return r.json()

# 4. Gene list pathway enrichment
def pathway_enrichment(gene_list):
    url = f"{ANALYSIS_URL}/identifiers/projection"
    genes_text = "\n".join(gene_list)
    headers = {"Content-Type": "text/plain"}
    r = requests.post(url, data=genes_text, headers=headers)
    r.raise_for_status()
    return r.json()

# 5. Look up a gene in Reactome
def query_gene(gene_symbol):
    url = f"{CONTENT_URL}/data/query/{gene_symbol}"
    r = requests.get(url, headers={"Accept": "application/json"})
    r.raise_for_status()
    return r.json()

# Example: DNA repair pathways
results = search_pathways("DNA repair")
entries = results.get("results", [])
for entry in entries[:5]:
    for e in entry.get("entries", []):
        print(f"{e.get('stId', 'N/A')}: {e.get('name', 'N/A')}")

# Pathway enrichment
enrichment = pathway_enrichment(["BRCA1", "BRCA2", "TP53", "ATM", "CHEK2"])
for p in enrichment.get("pathways", [])[:5]:
    name = p.get("name", "N/A")
    pval = p.get("entities", {}).get("pValue", "N/A")
    found = p.get("entities", {}).get("found", 0)
    print(f"{name} — p={pval:.2e}, {found} genes found")