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🧬 BioQuery is in beta. We'd love your feedback!
APIAPI Overview

API Overview

The BioQuery API allows you to run queries programmatically and integrate cancer genomics analysis into your workflows.

The API is currently in beta and available only to users with Researcher access. Contact us to request access.

Base URL

https://api.bioquery.io/v1

Quick Start

1. Get an API Key

  1. Sign in to bioquery.io 
  2. Go to Settings → API Keys
  3. Click Generate New Key
  4. Copy and store your key securely

2. Make Your First Request

curl -X POST https://api.bioquery.io/v1/query \
  -H "Authorization: Bearer YOUR_API_KEY" \
  -H "Content-Type: application/json" \
  -d '{"query": "Is DDR1 higher in KIRP vs KIRC?"}'

3. Get Your Results

{
  "id": "card_abc123",
  "status": "completed",
  "query": {
    "original": "Is DDR1 higher in KIRP vs KIRC?",
    "parsed": {
      "gene": "DDR1",
      "cancer_types": ["KIRP", "KIRC"],
      "analysis_type": "differential_expression"
    }
  },
  "results": {
    "answer": "DDR1 expression is significantly higher in papillary RCC (KIRP) compared to clear cell RCC (KIRC)...",
    "statistics": {
      "p_value": 0.00032,
      "fold_change": 2.3
    }
  }
}

Key Concepts

Query Cards

The API returns Query Card objects containing:

  • Natural language answer
  • Statistical results
  • Figure data (Plotly JSON)
  • Methods text
  • SQL query

Synchronous vs Asynchronous

  • Simple queries: Return results immediately (~5-10 seconds)
  • Complex queries: Return a card_id for polling

Rate Limits

TierRequests/DayConcurrent
Free21
Researcher1005
EnterpriseCustomCustom

SDKs

Python

pip install bioquery
from bioquery import BioQuery
 
client = BioQuery(api_key="YOUR_API_KEY")
result = client.query("Is DDR1 higher in KIRP vs KIRC?")
 
print(result.answer)
print(result.statistics)

R (Coming Soon)

An R package is in development. Sign up to be notified when it’s available.

Next Steps

Welcome to BioQueryAuthentication