AGNXIAgent Skills

reactome-database

davila7

Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.

Quick Install

bunx add-skill davila7/claude-code-templates -s reactome-database

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Instructions

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uv pip install reactome2py

import requests

response = requests.get("https://reactome.org/ContentService/data/database/version")
version = response.text
print(f"Reactome version: {version}")

import requests

entity_id = "R-HSA-69278"  # Example pathway ID
response = requests.get(f"https://reactome.org/ContentService/data/query/{entity_id}")
data = response.json()

import requests

event_id = "R-HSA-69278"
response = requests.get(
    f"https://reactome.org/ContentService/data/event/{event_id}/participatingPhysicalEntities"
)
molecules = response.json()

import reactome2py
from reactome2py import content

# Query pathway information
pathway_info = content.query_by_id("R-HSA-69278")

# Get database version
version = content.get_database_version()

import requests

# Prepare identifier list
identifiers = ["TP53", "BRCA1", "EGFR", "MYC"]
data = "\n".join(identifiers)

# Submit analysis
response = requests.post(
    "https://reactome.org/AnalysisService/identifiers/",
    headers={"Content-Type": "text/plain"},
    data=data
)

result = response.json()
token = result["summary"]["token"]  # Save token to retrieve results later

# Access pathways
for pathway in result["pathways"]:
    print(f"{pathway['stId']}: {pathway['name']} (p-value: {pathway['entities']['pValue']})")

# Token is valid for 7 days
response = requests.get(f"https://reactome.org/AnalysisService/token/{token}")
results = response.json()

#Gene	Sample1	Sample2	Sample3
TP53	2.5	3.1	2.8
BRCA1	1.2	1.5	1.3
EGFR	4.5	4.2	4.8

import requests

# Read TSV file
with open("expression_data.tsv", "r") as f:
    data = f.read()

response = requests.post(
    "https://reactome.org/AnalysisService/identifiers/",
    headers={"Content-Type": "text/plain"},
    data=data
)

result = response.json()

response = requests.post(
    "https://reactome.org/AnalysisService/identifiers/projection/",
    headers={"Content-Type": "text/plain"},
    data=data
)

token = result["summary"]["token"]
pathway_id = "R-HSA-69278"
url = f"https://reactome.org/PathwayBrowser/#{pathway_id}&DTAB=AN&ANALYSIS={token}"
print(f"View results: {url}")

# Query pathway information
python scripts/reactome_query.py query R-HSA-69278

# Perform overrepresentation analysis
python scripts/reactome_query.py analyze gene_list.txt

# Get database version
python scripts/reactome_query.py version