PubMed Evidence Table: Study Designs, Retraction Screening, PRISMA Counts & Rayyan/Covidence Import

Run your PubMed searches and get a screening-ready Excel evidence table. Each article comes with its study design, a sample size quoted from the abstract, its retraction and correction status, and PMID, DOI and PMC links. You also get PRISMA-style counts and import files for Rayyan, Covidence, EndNote and Zotero.

Most PubMed exports are raw dumps that someone then spends hours tidying in Excel. PubMed Evidence Table does the mechanical part and leaves the judgement to you. It queries PubMed through NCBI's official E-utilities API, tags study designs from NLM's own indexing, screens every article against PubMed and Crossref retraction notices (including Retraction Watch data), and records how many records each filter removed.

• 🔎 Your exact PubMed syntax, with one or more search strings. Overlaps are de-duplicated and counted
• 🧪 Study design from NLM indexing: RCT (with trial phase), meta-analysis, systematic review, cohort, case-control, cross-sectional, case report, guideline, review. If PubMed hasn't indexed a record yet, the field stays blank rather than guessed
• 👥 Population tags from MeSH (age groups, sex, humans or animals) and a sample size quoted from the abstract with a confidence level and the exact sentence it came from, left blank when the abstract is ambiguous
• 🚦 Retraction screen: OK, CHECK (expression of concern, preprint, or a notice record) or FIX (retracted). Errata are noted
• 📊 PRISMA-style counts: records identified, removed by each filter, duplicates removed, records over your limit, retracted records excluded, and records left for screening. The numbers always add up
• 📥 Import files: RIS (Rayyan, Covidence, EndNote, Zotero), Rayyan CSV, and the original PubMed-format text straight from NCBI
• 🧾 Search log: each query as written, the final search string, PubMed's own translation of it, and the date, ready for your methods section
• 💸 $0.004 per returned article. 200 articles cost $0.80. Searches with no results cost nothing

Who it's for

• Medical writers and med-affairs teams: evidence tables for literature reviews, publication plans and value dossiers
• Clinicians, pharmacists and guideline groups: a fast, structured first pass over the evidence on a question
• HEOR, market-access and consulting analysts: reproducible PubMed searches with counts you can report
• Systematic-review teams: run the searches, then screen in Rayyan or Covidence with the counts already logged

Not for coursework or ghostwriting. This tool searches, organizes and screens records. It doesn't write reviews, judge study quality or extract outcomes, and it isn't meant for completing assignments or academic work on someone else's behalf. Every included study still needs a human to read it.

How to use it

1. Click Try for free and paste one or more PubMed search strings, written exactly as you would in PubMed ([tiab], [mh], [pt], AND / OR / NOT).
2. Optional: add filters, such as publication dates, study designs, languages, animal-only exclusion, abstract required or free full text. Each filter's effect is counted.
3. Set Maximum articles. You pay per returned article, so this also caps the cost.
4. Click Start. 200 articles usually take under a minute without an NCBI key.
5. Download EVIDENCE_TABLE_XLSX from Storage → Key-value store. Import REVIEW_IMPORT_RIS or REVIEW_IMPORT_RAYYAN_CSV into your screening tool.

Input example

{
  "queries": [
    "semaglutide[tiab] AND obesity[tiab]",
    "semaglutide[tiab] AND (weight loss[tiab] OR body weight[mh])"
  ],
  "dateFrom": "2020",
  "dateTo": "2025",
  "studyDesigns": ["rct", "meta-analysis", "systematic-review"],
  "excludeAnimalOnly": true,
  "languages": ["english"],
  "retractedArticles": "flag",
  "maxResults": 60,
  "citationStyle": "vancouver"
}

Output example

Real output from a platform run of the input above:

PRISMA-style counts (PRISMA_COUNTS / Excel sheet)

Stage	Records
Records identified (PubMed, 2 queries)	5,419
Removed by filter: publication date 2020–2025	2,001
Removed by filter: study design (RCT, meta-analysis, systematic review)	2,911
Removed by filter: language English	4
Duplicates removed (found by both queries)	198
Not included (maximum articles reached)	245
Records for screening	60

Evidence table rows (shortened)

Status	Citation (Vancouver, shortened here)	Study design	Sample size (confidence)	Quote
OK	Wilding JPH, Batterham RL, Calanna S, et al. Once-Weekly Semaglutide in Adults with Overweight or Obesity. N Engl J Med. 2021;384(11):989–1002.	Randomized controlled trial	1,961 adults (high)	"…we enrolled 1961 adults with a body-mass index…"
OK	Lincoff AM, Brown-Frandsen K, Colhoun HM, et al. Semaglutide and Cardiovascular Outcomes in Obesity without Diabetes. N Engl J Med. 2023;389(24):2221–32.	Randomized controlled trial	17,604 patients (high)	"…A total of 17,604 patients were enrolled…"
OK	Tan HC, Dampil OA, Marquez MM. Efficacy and Safety of Semaglutide for Weight Loss in Obesity Without Diabetes: A Systematic Review and Meta-Analysis. J ASEAN Fed Endocr Soc. 2022;37(2):65–72.	Meta-analysis	4 studies (medium); note: pooled participants 3,613	"…The study included 4 randomized controlled trials having a total of 3,613 individuals…"
OK	PMID 35441470 (its abstract reports two different group sizes)	Randomized controlled trial	blank (unclear: 327 and 1,961)	n/a: extract by hand

A retracted trial, as the screen reports it:

{
  "status": "FIX",
  "title": "RETRACTED: Hydroxychloroquine in the Treatment of COVID-19: A Multicenter Randomized Controlled Study.",
  "studyDesign": "Randomized controlled trial",
  "retractionStatus": "Retracted",
  "notices": [
    {"source": "PubMed", "type": "RetractionIn"},
    {"source": "Crossref (Retraction Watch)", "type": "retraction"}
  ],
  "notes": ["RETRACTED. Exclude it, or report it as retracted."]
}

The Excel evidence table

Column group	What's in it
Citation, year, journal	Formatted in your chosen style (Vancouver by default) with citeproc-js and the official CSL style
Study design + source	From PubMed publication types or MeSH, with the source named. Blank when PubMed hasn't indexed it
Population tags	MeSH age, sex and species check tags (e.g. Humans, Adult, Aged, Female)
Sample size, unit, confidence, quote	Copied from the abstract only when it is stated clearly. high = an explicit total or enrolment statement; medium = one clear statement; low = only an "n =" mention; blank = unclear or not stated
Outcomes, Include/Exclude, Reason, Notes	Left empty for the reviewer (shaded)
Retraction / correction status, flags	Retracted, expression of concern, corrected (erratum), notice record, or none found
PMID, PubMed, DOI and PMC links	Clickable
Publication types, major MeSH, title, authors, abstract	For screening and filtering in Excel

Other sheets: PRISMA counts, Search strategy (queries, final strings, PubMed translations, per-filter counts) and Read me (column definitions and caveats).

What OK, CHECK and FIX mean

Status	Meaning
🟢 OK	No retraction or expression of concern found in PubMed or Crossref. Errata are noted but don't change the status
🟡 CHECK	Partial retraction, expression of concern, preprint, or a record that is itself a retraction, erratum or concern notice
🔴 FIX	Retracted (PubMed "Retracted Publication" / RetractionIn, or a Crossref / Retraction Watch notice). Left out of the citations file

"OK" means no notice was found. It isn't a quality rating. To check a finished manuscript's reference list, use our Reference Checker.

Files you get

Key-value store key	What it is
EVIDENCE_TABLE_XLSX	Excel evidence table plus PRISMA, search strategy and read-me sheets
EVIDENCE_TABLE_CSV	The evidence table as CSV
PRISMA_COUNTS	Identification-stage counts as JSON (with an arithmetic check)
REVIEW_IMPORT_RIS	RIS for Rayyan, Covidence, EndNote, Zotero, Mendeley (abstract, MeSH keywords, PMID, DOI). The recommended import file
REVIEW_IMPORT_RAYYAN_CSV	CSV in Rayyan's column layout (key, title, authors, abstract, doi, pubmed_id, pmc_id…)
PUBMED_MEDLINE_TXT	The records in PubMed (MEDLINE) text format, straight from NCBI. It's the same format as PubMed's Save → Format: PubMed, so save it as a .txt file for Covidence or Rayyan
CITATIONS	Bibliography in your chosen style (retracted articles left out)
SUMMARY	Search log, PRISMA counts, design breakdown and API stats

Pricing

$0.004 per article returned (pay-per-event). Design tags, sample-size quotes, the retraction screen, citations and all export files are included.

Articles	Cost
50	$0.20
200	$0.80
1,000	$4.00

Searches with no results cost nothing. If you choose Exclude for retracted articles, they are removed before you're charged. The Actor also never fetches more articles than your maximum charge per run allows.

Limits, honestly

• Study design depends on NLM indexing. Very recent articles are often not indexed yet, so their design is blank and flagged. We never infer a design from the abstract.
• Sample size is a quote, not an extraction. We copy a number only when the abstract states it unambiguously, show you the sentence, and leave it blank otherwise. Always confirm against the full text.
• Outcomes, risk of bias and inclusion decisions are yours. Those columns stay empty.
• PRISMA counts cover identification only. Screening and eligibility happen in your review tool.
• PubMed returns at most 9,999 records per search string. Anything beyond that is counted, and the fix is to split the search by date.
• One database. This searches PubMed/MEDLINE only. A systematic review usually needs more (Embase, CENTRAL, trial registries).

FAQ

Does it work without an NCBI API key? Yes. It identifies itself to NCBI as required and stays under NCBI's limit of 3 requests per second. Adding your own free NCBI key makes large searches faster.

Will my search give the same results as the PubMed website? The same search string gives the same records. The Search strategy sheet shows PubMed's own translation of each query, so you can reproduce it. Counts change over time as PubMed adds records, which is why the date is logged.

Can AI agents use it? Yes, through the Apify API, the Python or JavaScript clients, or Apify's MCP server. Each run returns structured JSON with designs, links and retraction flags.

Data sources and credits

• PubMed / MEDLINE, U.S. National Library of Medicine, through NCBI E-utilities. Not affiliated with or endorsed by NLM/NCBI
• Crossref for retraction, correction and expression-of-concern notices, including Retraction Watch data
• citeproc-js and the CSL project styles (CC BY-SA 3.0) for citations

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Built by Panda Federation

Self-healing, local-first AI systems and data tools that run themselves.

The Panda Federation research toolkit:

• PubMed Evidence Table: screening-ready evidence tables from PubMed
• Literature Search: a Google Scholar alternative across 250M+ papers, with retraction screening
• Citation Formatter: DOIs, ISBNs and messy references to APA, MLA, Chicago, Harvard, IEEE, Vancouver, BibTeX and RIS
• Reference Checker: fake citations and retracted papers, found

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