Searching Clinicaltrials

Searching ClinicalTrials.gov (v2 REST API)

Query ClinicalTrials.gov — the U.S. registry of clinical studies — for trials matching a condition, intervention, and recruitment status. This skill uses the modern v2 REST API (/api/v2/studies), which returns structured JSON and paginates with an opaque cursor (pageToken), not page numbers.

The v2 API is fully public: no API key, no registration, no license barrier. The legacy v1/classic API and the older query_term-style endpoints are deprecated — do not build on them.

When to use

• OpenMed extracted a diagnosis ("metastatic colorectal cancer") or a drug ("pembrolizumab") and you want open trials for it.
• You are building a patient-to-trial matching feature and need candidate studies before applying eligibility logic (parsing-trial-eligibility).
• You need a corpus of trial records (eligibility text, outcomes) to feed back into openmed.analyze_text for biomedical NER.

If you already have an NCT number, fetch the single study directly (/api/v2/studies/NCT01234567) instead of searching.

Quick start (real v2 API call)

Base URL: https://clinicaltrials.gov/api/v2. No auth. JSON by default.

import requests

BASE = "https://clinicaltrials.gov/api/v2"

def search_trials(condition: str, intervention: str | None = None,
                  status: str = "RECRUITING", page_size: int = 50) -> dict:
    """One page of studies for a condition (+ optional intervention)."""
    params = {
        "query.cond": condition,            # condition / disease search
        "filter.overallStatus": status,     # comma-separated enum values
        "pageSize": min(page_size, 1000),   # max 1000; default 10
        "countTotal": "true",               # include totalCount on first page
        "format": "json",
    }
    if intervention:
        params["query.intr"] = intervention  # drug / intervention search
    r = requests.get(f"{BASE}/studies", params=params, timeout=30)
    r.raise_for_status()
    return r.json()

data = search_trials("breast cancer", intervention="trastuzumab")
print(data["totalCount"])                    # total matches (first page only)
for study in data["studies"]:
    ps = study["protocolSection"]
    nct = ps["identificationModule"]["nctId"]
    title = ps["identificationModule"]["briefTitle"]
    print(nct, "-", title)

Equivalent cURL:

curl "https://clinicaltrials.gov/api/v2/studies?query.cond=breast+cancer\
&query.intr=trastuzumab&filter.overallStatus=RECRUITING&pageSize=50&format=json"

Response shape

Top level: studies (array), nextPageToken (present only if more results), and totalCount (only when countTotal=true, on the first page). Each study is a protocolSection of typed modules:

Cursor pagination

There are no page numbers. Loop until nextPageToken is absent. The token is opaque — pass it back verbatim. Do not re-send countTotal after page 1.

def iter_all(condition: str, status: str = "RECRUITING"):
    params = {"query.cond": condition, "filter.overallStatus": status,
              "pageSize": 1000, "format": "json"}
    while True:
        r = requests.get(f"{BASE}/studies", params=params, timeout=30)
        r.raise_for_status()
        page = r.json()
        yield from page.get("studies", [])
        token = page.get("nextPageToken")
        if not token:
            break
        params["pageToken"] = token        # cursor for the next page

Trimming payloads

Default responses are large. Restrict to the fields you need with fields (dotted paths or module names) to cut bandwidth:

params["fields"] = ("NCTId,BriefTitle,OverallStatus,"
                    "Condition,EligibilityCriteria")

Workflow

1. Build the query from OpenMed facts. Map extracted Disease spans → query.cond; Pharmaceutical spans → query.intr. Free-text keywords go in query.term. Combine status filters as filter.overallStatus=RECRUITING,NOT_YET_RECRUITING.
2. Page through with the cursor until nextPageToken is gone; cap total pulls.
3. Persist nctId, status, conditions, interventions, and the raw eligibility text. Eligibility goes to parsing-trial-eligibility.
4. Optionally re-NER the eligibility / outcomes text with openmed.analyze_text to structure inclusion criteria.

Hand-off to / from OpenMed

• From OpenMed → trial search. openmed.analyze_text(note, model_name="disease_detection_superclinical") yields Disease and Pharmaceutical entities. Use the surface forms (or a grounded term from coding-icd10 / normalizing-rxnorm) as query.cond / query.intr.
• Trial text → OpenMed. Feed eligibilityModule.eligibilityCriteria and brief summaries back through openmed.analyze_text to extract conditions, meds, and labs mentioned in the criteria. Then hand to parsing-trial-eligibility for inclusion/exclusion matching against patient facts.
• Keep patient data local. The API call carries only the query terms (condition/drug names), never the patient note or any PHI.

Edge cases & gotchas

• Synonyms & spelling. The condition matcher is fuzzy but not infinite — "MI" will not match "myocardial infarction". Normalize OpenMed output first (ICD-10 / RxNorm) and consider issuing a few synonym variants.
• Status enums are exact. Valid values include RECRUITING, NOT_YET_RECRUITING, ENROLLING_BY_INVITATION, ACTIVE_NOT_RECRUITING, COMPLETED, SUSPENDED, TERMINATED, WITHDRAWN, UNKNOWN. Comma-separate; do not lowercase.
• totalCount is first-page only. Request countTotal=true once; it is not repeated on subsequent pages.
• Page size cap is 1000. Larger values are silently clamped.
• Rate limits. No key required, but throttle politely (a short sleep between pages); aggressive scraping can be blocked. For bulk/offline work, consider the full registry data dump rather than thousands of paged calls.
• pageToken expires if the underlying index shifts; restart the query if a token is rejected.
• Not medical advice. A trial appearing in results does not mean the patient qualifies — eligibility is decided downstream and reviewed by a clinician.

Standards & references

• ClinicalTrials.gov API v2 — https://clinicaltrials.gov/data-api/api
• Study data structure (modules / field paths) — https://clinicaltrials.gov/data-api/about-api/study-data-structure
• Search areas & query syntax — https://clinicaltrials.gov/data-api/about-api/search-areas
• OpenAPI / interactive reference — https://clinicaltrials.gov/api/v2/