davila7
Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.
bunx add-skill davila7/claude-code-templates -s clinicaltrials-databaseLoading…
ClinicalTrials.gov is a comprehensive registry of clinical studies conducted worldwide, maintained by the U.S. National Library of Medicine. Access API v2 to search for trials, retrieve detailed study information, filter by various criteria, and export data for analysis. The API is public (no authentication required) with rate limits of ~50 requests per minute, supporting JSON and CSV formats.
This skill should be used when working with clinical trial data in scenarios such as:
Search for clinical trials using the helper script:
cd scientific-databases/clinicaltrials-database/scripts
python3 query_clinicaltrials.py
Or use Python directly with the requests library:
import requests
url = "https://clinicaltrials.gov/api/v2/studies"
params = {
"query.cond": "breast cancer",
"filter.overallStatus": "RECRUITING",
"pageSize": 10
}
response = requests.get(url, params=params)
data = response.json()
print(f"Found {data['totalCount']} trials")
Get detailed information about a trial using its NCT ID:
import requests
nct_id = "NCT04852770"
url = f"https://clinicaltrials.gov/api/v2/studies/{nct_id}"
response = requests.get(url)
study = response.json()
# Access specific modules
title = study['protocolSection']['identificationModule']['briefTitle']
status = study['protocolSection']['statusModule']['overallStatus']
Find trials studying specific medical conditions or diseases using the query.cond parameter.
Example: Find recruiting diabetes trials
from scripts.query_clinicaltrials import search_studies
results = search_studies(
condition="type 2 diabetes",
status="RECRUITING",
page_size=20,
sort="LastUpdatePostDate:desc"
)
print(f"Found {results['totalCount']} recruiting diabetes trials")
for study in results['studies']:
protocol = study['protocolSection']
nct_id = protocol['identificationModule']['nctId']
title = protocol['identificationModule']['briefTitle']
print(f"{nct_id}: {title}")
Common use cases:
Search for trials testing specific interventions, drugs, devices, or procedures using the query.intr parameter.
Example: Find Phase 3 trials testing Pembrolizumab
from scripts.query_clinicaltrials import search_studies
results = search_studies(
intervention="Pembrolizumab",
status=["RECRUITING", "ACTIVE_NOT_RECRUITING"],
page_size=50
)
# Filter by phase in results
phase3_trials = [
study for study in results['studies']
if 'PHASE3' in study['protocolSection'].get('designModule', {}).get('phases', [])
]
Common use cases:
Find trials in specific locations using the query.locn parameter.
Example: Find cancer trials in New York
from scripts.query_clinicaltrials import search_studies
results = search_studies(
condition="cancer",
location="New York",
status="RECRUITING",
page_size=100
)
# Extract location details
for study in results['studies']:
locations_module = study['protocolSection'].get('contactsLocationsModule', {})
locations = locations_module.get('locations', [])
for loc in locations:
if 'New York' in loc.get('city', ''):
print(f"{loc['facility']}: {loc['city']}, {loc.get('state', '')}")
Common use cases:
Find trials conducted by specific organizations using the query.spons parameter.
Example: Find trials sponsored by NCI
from scripts.query_clinicaltrials import search_studies
results = search_studies(
sponsor="National Cancer Institute",
page_size=100
)
# Extract sponsor information
for study in results['studies']:
sponsor_module = study['protocolSection']['sponsorCollaboratorsModule']
lead_sponsor = sponsor_module['leadSponsor']['name']
collaborators = sponsor_module.get('collaborators', [])
print(f"Lead: {lead_sponsor}")
if collaborators:
print(f" Collaborators: {', '.join([c['name'] for c in collaborators])}")
Common use cases:
Filter trials by recruitment or completion status using the filter.overallStatus parameter.
Valid status values:
RECRUITING - Currently recruiting participantsNOT_YET_RECRUITING - Not yet open for recruitmentENROLLING_BY_INVITATION - Only enrolling by invitationACTIVE_NOT_RECRUITING - Active but no longer recruitingSUSPENDED - Temporarily haltedTERMINATED - Stopped prematurelyCOMPLETED - Study has concludedWITHDRAWN - Withdrawn prior to enrollmentExample: Find recently completed trials with results
from scripts.query_clinicaltrials import search_studies
results = search_studies(
condition="alzheimer disease",
status="COMPLETED",
sort="LastUpdatePostDate:desc",
page_size=50
)
# Filter for trials with results
trials_with_results = [
study for study in results['studies']
if study.get('hasResults', False)
]
print(f"Found {len(trials_with_results)} completed trials with results")
Get comprehensive information about specific trials including eligibility criteria, outcomes, contacts, and locations.
Example: Extract eligibility criteria
from scripts.query_clinicaltrials import get_study_details
study = get_study_details("NCT04852770")
eligibility = study['protocolSection']['eligibilityModule']
print(f"Eligible Ages: {eligibility.get('minimumAge')} - {eligibility.get('maximumAge')}")
print(f"Eligible Sex: {eligibility.get('sex')}")
print(f"\nInclusion Criteria:")
print(eligibility.get('eligibilityCriteria'))
Example: Extract contact information
from scripts.query_clinicaltrials import get_study_details
study = get_study_details("NCT04852770")
contacts_module = study['protocolSection']['contactsLocationsModule']
# Overall contacts
if 'centralContacts' in contacts_module:
for contact in contacts_module['centralContacts']:
print(f"Contact: {contact.get('name')}")
print(f"Phone: {contact.get('phone')}")
print(f"Email: {contact.get('email')}")
# Study locations
if 'locations' in contacts_module:
for location in contacts_module['locations']:
print(f"\nFacility: {location.get('facility')}")
print(f"City: {location.get('city')}, {location.get('state')}")
if location.get('status'):
print(f"Status: {location['status']}")
Handle large result sets efficiently using pagination.
Example: Retrieve all matching trials
from scripts.query_clinicaltrials import search_with_all_results
# Get all trials (automatically handles pagination)
all_trials = search_with_all_results(
condition="rare disease",
status="RECRUITING"
)
print(f"Retrieved {len(all_trials)} total trials")
Example: Manual pagination with control
from scripts.query_clinicaltrials import search_studies
all_studies = []
page_token = None
max_pages = 10 # Limit to avoid excessive requests
for page in range(max_pages):
results = search_studies(
condition="cancer",
page_size=1000, # Max page size
page_token=page_token
)
all_studies.extend(results['studies'])
# Check for next page
page_token = results.get('pageToken')
if not page_token:
break
print(f"Retrieved {len(all_studies)} studies across {page + 1} pages")
Export trial data to CSV format for analysis in spreadsheet software or data analysis tools.
Example: Export to CSV file
from scripts.query_clinicaltrials import search_studies
# Request CSV format
results = search_studies(
condition="heart disease",
status="RECRUITING",
format="csv",
page_size=1000
)
# Save to file
with open("heart_disease_trials.csv", "w") as f:
f.write(results)
print("Data exported to heart_disease_trials.csv")
Note: CSV format returns a string instead of JSON dictionary.
Extract key information for quick overview or reporting.
Example: Create trial summary
from scripts.query_clinicaltrials import get_study_details, extract_study_summary
# Get details and extract summary
study = get_study_details("NCT04852770")
summary = extract_study_summary(study)
print(f"NCT ID: {summary['nct_id']}")
print(f"Title: {summary['title']}")
print(f"Status: {summary['status']}")
print(f"Phase: {', '.join(summary['phase'])}")
print(f"Enrollment: {summary['enrollment']}")
print(f"Last Update: {summary['last_update']}")
print(f"\nBrief Summary:\n{summary['brief_summary']}")
Combine multiple filters for targeted searches.
Example: Multi-criteria search
from scripts.query_clinicaltrials import search_studies
# Find Phase 2/3 immunotherapy trials for lung cancer in California
results = search_studies(
condition="lung cancer",
intervention="immunotherapy",
location="California",
status=["RECRUITING", "NOT_YET_RECRUITING"],
page_size=100
)
# Further filter by phase
phase2_3_trials = [
study for study in results['studies']
if any(phase in ['PHASE2', 'PHASE3']
for phase in study['protocolSection'].get('designModule', {}).get('phases', []))
]
print(f"Found {len(phase2_3_trials)} Phase 2/3 immunotherapy trials")
Comprehensive Python script providing helper functions for common query patterns:
search_studies() - Search for trials with various filtersget_study_details() - Retrieve full information for a specific trialsearch_with_all_results() - Automatically paginate through all resultsextract_study_summary() - Extract key information for quick overviewRun the script directly for example usage:
python3 scripts/query_clinicaltrials.py
Detailed API documentation including:
Load this reference when working with unfamiliar API features or troubleshooting issues.
The API has a rate limit of approximately 50 requests per minute. For bulk data retrieval:
import time
import requests
def search_with_rate_limit(params):
try:
response = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params)
response.raise_for_status()
return response.json()
except requests.exceptions.HTTPError as e:
if e.response.status_code == 429:
print("Rate limited. Waiting 60 seconds...")
time.sleep(60)
return search_with_rate_limit(params) # Retry
raise
The API response has a nested structure. Key paths to common information:
study['protocolSection']['identificationModule']['nctId']study['protocolSection']['identificationModule']['briefTitle']study['protocolSection']['statusModule']['overallStatus']study['protocolSection']['designModule']['phases']study['protocolSection']['eligibilityModule']study['protocolSection']['contactsLocationsModule']['locations']study['protocolSection']['armsInterventionsModule']['interventions']Always implement proper error handling for network requests:
import requests
try:
response = requests.get(url, params=params, timeout=30)
response.raise_for_status()
data = response.json()
except requests.exceptions.HTTPError as e:
print(f"HTTP error: {e.response.status_code}")
except requests.exceptions.RequestException as e:
print(f"Request failed: {e}")
except ValueError as e:
print(f"JSON decode error: {e}")
Not all trials have complete information. Always check for field existence:
# Safe navigation with .get()
phases = study['protocolSection'].get('designModule', {}).get('phases', [])
enrollment = study['protocolSection'].get('designModule', {}).get('enrollmentInfo', {}).get('count', 'N/A')
# Check before accessing
if 'resultsSection' in study:
# Process results
pass
https://clinicaltrials.gov/api/v2For complete technical details, see references/api_reference.md.
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