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Compare ClinicalTrials.gov studies with PubMed citations for evidence gaps

PubMed & Clinical Trials Evidence Gap Report compares ClinicalTrials.gov records with PubMed citation metadata. Biomedical research, medical affairs, and evidence teams enter watchlists, NCT IDs, and PubMed queries. Outputs are source-linked evidence rows, gap alerts, reports, and exports. They are descriptive citation metadata — not medical conclusions, treatment guidance, article full text, or abstracts.

Live schema default dryRun is true: Start with defaults returns illustrative rows, does not call NCBI, and does not bill. Set dryRun false for a capped live run after preview.

This independent Actor is not affiliated with, sponsored by, or endorsed by NCBI, PubMed, or ClinicalTrials.gov.

from $8.00 / 1,000 biomedical evidence rows ($0.008 per evidence row; $0.15 per gap alert; $5.00 per report; $3.00 per export)

Open PubMed & Clinical Trials Evidence Gap Report on Apify

Trial↔PubMed evidence gaps, not PubMed-only watch and not news RSS

Use this page when the job is matching ClinicalTrials.gov studies to PubMed citations and emitting gap alerts or reports. Use PubMed Literature Watch & Research Report for PubMed-only citation monitors and literature-update reports. Use OpenAlex Scholarly Works Scraper for broader OpenAlex discovery. Use NIH RePORTER Funding Landscape Report for NIH awards. Use Google News Scraper for news headlines.

Use cases

• Evidence-gap finding: compare NCT studies with PubMed citation metadata.
• Watch NCT/condition/intervention portfolios with a stable monitorKey.
• Low-cost paid trial: one NCT, raw row plus optional gap alert, cap at $0.50.
• Screening export after the trial path proves useful.
• Downstream of NIH funding / grant-publication Actors named in the README.

How is PubMed & Clinical Trials Evidence Gap Report different from PubMed Literature Watch?

This Actor compares ClinicalTrials.gov studies with PubMed citation metadata and can emit evidence rows, evidence-gap alerts, a biomedical evidence report, and an export. Store ID taroyamada/biomedical-trial-literature-evidence-report. PubMed Literature Watch is NCBI E-utilities citation watch, literature-update reports, and new-PMID alerts without ClinicalTrials.gov matching. OpenAlex Scholarly Works Scraper is the official OpenAlex API, not trial matching. NIH RePORTER Funding Landscape Report is NIH awards. Google News Scraper is news RSS. Citation metadata only — not full text or abstracts. Not medical advice.

What is the best first run?

Live schema default dryRun is true. Hitting Start with defaults does not call NCBI and does not bill. For a capped live trial, the published README uses this input. It can deliver a biomedical-evidence-row at $0.008 and an evidence-gap-alert at $0.15 when the starter evidence matches. A zero-row run has zero event charge:

{
  "searchTerms": [],
  "watchlists": [
    {
      "id": "starter-study",
      "nctIds": ["NCT04280705"],
      "maxStudies": 1
    }
  ],
  "fromDate": "2025",
  "sort": "most_recent",
  "maxResultsPerQuery": 1,
  "maxArticles": 1,
  "maxStudiesPerWatchlist": 1,
  "maxPagesPerWatchlist": 1,
  "runMode": "monitor",
  "monitorKey": "starter-nct04280705-v2",
  "initialRunMode": "emit_backfill",
  "emitRawRows": true,
  "generateReport": false,
  "generateExport": false,
  "emitUnchanged": false,
  "maxChargeUsd": 0.5,
  "dryRun": false
}

When that result fits, the published full-report path uses a separate monitorKey, generateReport true, generateExport true, emitRawRows false, and maxChargeUsd 8.41 ($5.00 report + $3.00 export, plus headroom). Unchanged monitoring runs still produce zero rows and zero event charge:

{
  "searchTerms": [],
  "watchlists": [
    {
      "id": "starter-study",
      "nctIds": ["NCT04280705"],
      "maxStudies": 1
    }
  ],
  "fromDate": "2025",
  "sort": "most_recent",
  "maxResultsPerQuery": 1,
  "maxArticles": 1,
  "maxStudiesPerWatchlist": 1,
  "maxPagesPerWatchlist": 1,
  "runMode": "monitor",
  "monitorKey": "starter-nct04280705-v2-full-report-v1",
  "initialRunMode": "emit_backfill",
  "emitRawRows": false,
  "generateReport": true,
  "generateExport": true,
  "emitUnchanged": false,
  "maxChargeUsd": 8.41,
  "dryRun": false
}

Published Store example run input omits dryRun; schema default true applies unless you override it. Live schema default initialRunMode is emit_backfill. README prose that still says the default is baseline_only is stale versus the live schema; prefer the schema.

Run PubMed & Clinical Trials Evidence Gap Report on Apify

What input is required?

The live schema has no required array. additionalProperties is false. README Quickstart JSON that sends watchlist conditions, interventions, and pubmedQuery is README documentation; the live items schema is not fully expanded. Prefer nctIds as in the paid-trial JSON above.

What does a result contain?

The published README sample is a literature_update_report row. It is a README illustration, not a live coverage guarantee:

{
  "rowType": "literature_update_report",
  "billingEventName": "biomedical-evidence-report",
  "query": {
    "searchTerms": ["cancer immunotherapy"],
    "fromDate": "2026"
  },
  "articleCount": 12,
  "pmids": ["39763750", "39763800"],
  "topJournals": [{"value": "Cancer Research", "count": 3}],
  "summary": "12 PubMed publications matched this literature update.",
  "sourceUrl": "https://pubmed.ncbi.nlm.nih.gov/"
}

Does this Actor return full text or medical conclusions?

No. Official NCBI ESearch and ESummary JSON; no browser scraping or login. Citation metadata only — not full text or abstracts. PubMed records can be incomplete or updated after publication. Optional NCBI API key; keyless mode is paced conservatively. Outputs are not medical advice, clinical efficacy claims, or a substitute for reviewing the source publication. Keep NCBI attribution and source URLs.

How is PubMed & Clinical Trials Evidence Gap Report priced?

Billing is pay per event. The live Store card is from $8.00 / 1,000 biomedical evidence rows. Current PPE:

There is no start charge. A baseline_only or unchanged monitor emits zero rows and zero event charge. Default dryRun true means a default Start does not bill. Do not run the $5.00 report under a cap that cannot cover it.

from $8.00 per 1,000 biomedical evidence rows; $0.15 per gap alert; $5.00 per report; $3.00 per export

See PubMed & Clinical Trials Evidence Gap Report pricing on Apify

Limits to keep in mind

• Default dryRun is true. Paid runs must set dryRun false.
• Live schema default initialRunMode is emit_backfill, not the README baseline_only sentence.
• Citation metadata only. Not full text, not abstracts, not medical advice.
• Not affiliated with NCBI, PubMed, or ClinicalTrials.gov.

Published README next-report Store listing (no local landing): NIH Grant Publication Linkage & Output Report on Apify.

Open PubMed & Clinical Trials Evidence Gap Report on Apify

Related pages

• PubMed Literature Watch & Research Report — PubMed-only citation watch and reports
• OpenAlex Scholarly Works Scraper — OpenAlex API discovery
• NIH RePORTER Funding Landscape Report — NIH awards, not trial↔PubMed matching
• HHS Healthcare Data Breach Change Scraper — HHS OCR disclosures, not literature
• TED, SAM.gov & Grants Bid Alerts Scraper — procurement notices, not ClinicalTrials.gov
• Google News Scraper — news RSS
• ClinicalTrials.gov Sponsor Pipeline Scraper — sponsor pipeline watches, not trial↔PubMed evidence gaps
• Clinical Trial & FDA Signal Alerts — openFDA + trials watches.
• Tools