alterlab-clinicaltrials

name	alterlab-clinicaltrials
description	Query ClinicalTrials.gov via its API v2 to search trials by condition, drug, location, recruitment status, or phase and retrieve trial details by NCT ID. Use when finding interventional or observational studies, checking trial status and eligibility for patient matching, or exporting clinical trial records for research. Part of the AlterLab Academic Skills suite.
license	MIT
allowed-tools	Read WebFetch Bash(curl:*) Bash(python:*)
compatibility	Keyless ClinicalTrials.gov API v2 (no authentication required)
metadata	{"skill-author":"AlterLab","version":"1.0.0"}

ClinicalTrials.gov Database

Overview

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.

When to Use This Skill

This skill should be used when working with clinical trial data in scenarios such as:

• Patient matching - Finding recruiting trials for specific conditions or patient populations
• Research analysis - Analyzing clinical trial trends, outcomes, or study designs
• Drug/intervention research - Identifying trials testing specific drugs or interventions
• Geographic searches - Locating trials in specific locations or regions
• Sponsor/organization tracking - Finding trials conducted by specific institutions
• Data export - Extracting clinical trial data for further analysis or reporting
• Trial monitoring - Tracking status updates or results for specific trials
• Eligibility screening - Reviewing inclusion/exclusion criteria for trials

Quick Start

Basic Search Query

Run the helper script (from this skill's scripts/ directory):

python3 scripts/query_clinicaltrials.py

Or use Python directly with the requests library. Note: the API omits totalCount unless you pass countTotal=true, and the pagination token is returned as nextPageToken.

import requests

url = "https://clinicaltrials.gov/api/v2/studies"
params = {
    "query.cond": "breast cancer",
    "filter.overallStatus": "RECRUITING",
    "pageSize": 10,
    "countTotal": "true",  # required for data['totalCount'] to exist
}

response = requests.get(url, params=params)
data = response.json()

print(f"Found {data['totalCount']} trials")

Retrieve Specific Trial

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']

Core Capabilities

1. Search by Condition/Disease

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:

• Finding trials for rare diseases
• Identifying trials for comorbid conditions
• Tracking trial availability for specific diagnoses

2. Search by Intervention/Drug

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', [])
]

Phase filtering note: There is no filter.phase query parameter — passing one returns HTTP 400. To filter server-side, use aggFilters=phase:N where N is 0–4 (values within a facet are space-separated, e.g. aggFilters=phase:2 3 for Phase 2 or 3), or filter.advanced=AREA[Phase](PHASE2 OR PHASE3) with Essie syntax. Post-filtering on designModule.phases (as above) is the simplest approach when you already need the full records.

Common use cases:

• Drug development tracking
• Competitive intelligence for pharmaceutical companies
• Treatment option research for clinicians

3. Geographic Search

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:

• Patient referrals to local trials
• Geographic trial distribution analysis
• Site selection for new trials

4. Search by Sponsor/Organization

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:

• Tracking institutional research portfolios
• Analyzing funding organization priorities
• Identifying collaboration opportunities

5. Filter by Study Status

Filter trials by recruitment or completion status using the filter.overallStatus parameter.

Valid status values:

• RECRUITING - Currently recruiting participants
• NOT_YET_RECRUITING - Not yet open for recruitment
• ENROLLING_BY_INVITATION - Only enrolling by invitation
• ACTIVE_NOT_RECRUITING - Active but no longer recruiting
• SUSPENDED - Temporarily halted
• TERMINATED - Stopped prematurely
• COMPLETED - Study has concluded
• WITHDRAWN - Withdrawn prior to enrollment

Example: 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")

6. Retrieve Detailed Study Information

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']}")

7. Pagination and Bulk Data Retrieval

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. The API returns the cursor as 'nextPageToken';
    # you pass it back in as the 'pageToken' request parameter.
    page_token = results.get('nextPageToken')
    if not page_token:
        break

print(f"Retrieved {len(all_studies)} studies across {page + 1} pages")

8. Data Export to CSV

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.

9. Extract and Summarize Study Information

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']}")

10. Combined Query Strategies

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")

Resources

• scripts/query_clinicaltrials.py — helpers for the common query patterns: search_studies(), get_study_details(), search_with_all_results() (auto-pagination), extract_study_summary(). Run directly for example usage.
• references/api_reference.md — full endpoint/parameter specs, response modules, error handling, and data standards (ISO 8601, CommonMark). Load when working with unfamiliar API features or troubleshooting.

Best Practices

Rate Limit Management

The API has a rate limit of approximately 50 requests per minute. For bulk data retrieval:

1. Use maximum page size (1000) to minimize requests
2. Implement exponential backoff on rate limit errors (429 status)
3. Add delays between requests for large-scale data collection

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

Data Structure Navigation

The API response has a nested structure. Key paths to common information:

• NCT ID: study['protocolSection']['identificationModule']['nctId']
• Title: study['protocolSection']['identificationModule']['briefTitle']
• Status: study['protocolSection']['statusModule']['overallStatus']
• Phase: study['protocolSection']['designModule']['phases']
• Eligibility: study['protocolSection']['eligibilityModule']
• Locations: study['protocolSection']['contactsLocationsModule']['locations']
• Interventions: study['protocolSection']['armsInterventionsModule']['interventions']

Error Handling

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}")

Handling Missing Data

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

Technical Specifications

• Base URL: https://clinicaltrials.gov/api/v2
• Authentication: Not required (public API)
• Rate Limit: ~50 requests/minute per IP
• Response Formats: JSON (default), CSV
• Max Page Size: 1000 studies per request
• Date Format: ISO 8601
• Text Format: CommonMark Markdown for rich text fields
• API Version: 2.0 (released March 2024)
• API Specification: OpenAPI 3.0

For complete technical details, see references/api_reference.md.