Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
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Reactome is a free, open-source, curated pathway database with 2,825+ human pathways. Query biological pathways, perform overrepresentation and expression analysis, map genes to pathways, explore molecular interactions via REST API and Python client for systems biology research.
This skill should be used when:
Reactome provides two main API services and a Python client library:
Query and retrieve biological pathway data, molecular interactions, and entity information.
Common operations:
API Base URL: https://reactome.org/ContentService
Perform computational analysis on gene lists and expression data.
Analysis types:
API Base URL: https://reactome.org/AnalysisService
Python client library that wraps Reactome API calls for easier programmatic access.
Installation:
uv pip install reactome2py
Note: The reactome2py package (version 3.0.0, released January 2021) is functional but not actively maintained. For the most up-to-date functionality, consider using direct REST API calls.
The Content Service uses REST protocol and returns data in JSON or plain text formats.
Get database version:
import requests
response = requests.get("https://reactome.org/ContentService/data/database/version")
version = response.text
print(f"Reactome version: {version}")
Query a specific entity:
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()
Get participating molecules in a pathway:
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()
For detailed API endpoints and parameters, refer to references/api_reference.md in this skill.
Submit a list of gene/protein identifiers to find enriched pathways.
Using REST API:
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']})")
Retrieve analysis by token:
# Token is valid for 7 days
response = requests.get(f"https://reactome.org/AnalysisService/token/{token}")
results = response.json()
Analyze gene expression datasets with quantitative values.
Input format (TSV with header starting with #):
#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
Submit expression data:
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()
Map identifiers to human pathways exclusively using the /projection/ endpoint:
response = requests.post(
"https://reactome.org/AnalysisService/identifiers/projection/",
headers={"Content-Type": "text/plain"},
data=data
)
Analysis results can be visualized in the Reactome Pathway Browser by constructing URLs with the analysis token:
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}")
GET /token/{TOKEN} endpoint to retrieve resultsReactome accepts various identifier formats:
The system automatically detects identifier types.
For overrepresentation analysis:
For expression analysis:
All API responses return JSON containing:
pathways: Array of enriched pathways with statistical metricssummary: Analysis metadata and tokenentities: Matched and unmapped identifiersThis skill includes scripts/reactome_query.py, a helper script for common Reactome operations:
# 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
For comprehensive API endpoint documentation, see references/api_reference.md in this skill.
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