reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
Reactome Database
Overview
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.
When to Use This Skill
This skill should be used when:
Core Capabilities
Reactome provides two main API services and a Python client library:
1. Content Service - Data Retrieval
Query and retrieve biological pathway data, molecular interactions, and entity information.
Common operations:
API Base URL: https://reactome.org/ContentService
2. Analysis Service - Pathway Analysis
Perform computational analysis on gene lists and expression data.
Analysis types:
API Base URL: https://reactome.org/AnalysisService
3. reactome2py Python Package
Python client library that wraps Reactome API calls for easier programmatic access.
Installation:
uv pip install reactome2pyNote: 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.
Querying Pathway Data
Using Content Service REST API
The Content Service uses REST protocol and returns data in JSON or plain text formats.
Get database version:
import requestsresponse = requests.get("https://reactome.org/ContentService/data/database/version")
version = response.text
print(f"Reactome version: {version}")
Query a specific entity:
import requestsentity_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 requestsevent_id = "R-HSA-69278"
response = requests.get(
f"https://reactome.org/ContentService/data/event/{event_id}/participatingPhysicalEntities"
)
molecules = response.json()
Using reactome2py Package
import reactome2py
from reactome2py import contentQuery 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.
Performing Pathway Analysis
Overrepresentation Analysis
Submit a list of gene/protein identifiers to find enriched pathways.
Using REST API:
import requestsPrepare 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()Expression Data Analysis
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 4.8Submit expression data:
import requestsRead 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()
Species Projection
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
)Visualizing Results
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}")Working with Analysis Tokens
GET /token/{TOKEN} endpoint to retrieve resultsData Formats and Identifiers
Supported Identifier Types
Reactome accepts various identifier formats:
The system automatically detects identifier types.
Input Format Requirements
For overrepresentation analysis:
For expression analysis:
Output Format
All API responses return JSON containing:
pathways: Array of enriched pathways with statistical metricssummary: Analysis metadata and tokenentities: Matched and unmapped identifiersHelper Scripts
This skill includes scripts/reactome_query.py, a helper script for common Reactome operations:
# Query pathway information
python scripts/reactome_query.py query R-HSA-69278Perform overrepresentation analysis
python scripts/reactome_query.py analyze gene_list.txtGet database version
python scripts/reactome_query.py versionAdditional Resources
For comprehensive API endpoint documentation, see references/api_reference.md in this skill.
Current Database Statistics (Version 94, September 2025)
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