Europe PMC Scraper - Papers, Abstracts & Citations

Scrape Europe PMC biomedical literature in bulk. Extract title, authors, affiliation, journal, DOI, PMID, PMCID, abstract, MeSH terms, keywords, citation counts and open-access status to CSV/JSON. No API key, no login.

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What does the Europe PMC Scraper do?

This Actor turns Europe PMC data into a structured dataset. You point it at by topic or open access, bounded by date, it walks the result pages one after another, and it writes one clean row per article into your dataset — ready to export as JSON, CSV or Excel, or to pull straight from the Apify API.

Europe PMC indexes PubMed, PMC, preprints and patents behind one keyless REST API, and the Actor reads it with resultType=core so abstracts, MeSH terms and affiliations come back in the same response as the citation metadata. Deep paging uses the cursor mark the API returns in the body, which is what lets a run walk past the 1,000-record wall that ordinary page numbers hit. Pagination is followed automatically until it runs out of results, hits your page limit or hits your Max items cap, whichever comes first. Every row is de-duplicated across the whole run, so you are never billed twice for the same article.

There is no API key, no login and no browser involved. That keeps runs fast and cheap, and it means you can schedule the Actor without worrying about credentials expiring.

Who is it for?

• Research and R&D teams monitoring publications on a topic.
• Systematic-review teams exporting a search for screening.
• AI and NLP teams assembling biomedical abstract corpora.
• Competitive-intelligence analysts tracking what rivals publish.
• Librarians and bibliometricians measuring output and citations.

Use cases

• Export every paper matching a topic with abstracts for screening.
• Rank a field's literature by citation count to find key work.
• Filter to open-access articles you can legally reuse in full.
• Build a biomedical abstract corpus for embedding or classification.
• Track how publication volume on a subject changed by year.

Why use this Europe PMC Scraper?

• 🔑 Keyless — no account, no API token, no cookies to paste.
• 📦 31 fields per article — everything the source exposes, already typed.
• 📄 Real pagination — it walks page after page instead of returning the first screen.
• 🎯 Precise caps — Max items stops the run exactly where you want it, so the bill is predictable.
• 📊 Export anywhere — JSON, CSV, Excel or HTML, plus the Apify API and integrations.
• 💸 Pay per result — you pay for rows you actually receive, with no platform fees to calculate.

What data can you extract?

Every run produces one row per article, with these fields:

Field	Type	Description
articleId	string	Europe PMC article identifier
source	string	Source database, e.g. MED, PMC or PPR
pmid	string	PubMed identifier
pmcid	string	PubMed Central identifier
doi	string	Digital Object Identifier
title	string	Article title
authorString	string	Full author list as published
firstAuthor	string	First author
affiliation	string	Affiliation of the first author when published
journalTitle	string	Journal title
journalAbbreviation	string	Medline journal abbreviation
issn	string	Journal ISSN
volume	string	Journal volume
issue	string	Journal issue
pageInfo	string	Page range
pubYear	number	Publication year
firstPublicationDate	string	Date of first publication
publicationTypes	string	Publication types, separated by a pipe
abstractText	string	Full abstract text
keywords	string	Author keywords, separated by a pipe
meshTerms	string	MeSH headings, separated by a pipe
citedByCount	number	Number of citing articles in Europe PMC
isOpenAccess	boolean	Whether the full text is open access
inEPMC	boolean	Whether full text is readable in Europe PMC
hasPdf	boolean	Whether a PDF is available
fullTextUrl	string	Best available full-text link
articleUrl	string	Europe PMC article page
language	string	Publication language
query	string	Search query this row came from
page	number	Result page the article appeared on
scrapedAt	string	ISO timestamp of extraction

Output example

{
  "abstractText": "Chikungunya virus (CHIKV) is transmitted by Aedes mosquitoes and causes outbreaks\u2026",
  "affiliation": "Department of Molecular Virology, Institute of Tropical Medicine",
  "articleId": "42734786",
  "articleUrl": "https://europepmc.org/article/MED/42734786",
  "authorString": "Zhang L, Ahmed S, Fern\u00e1ndez M, Okafor C.",
  "citedByCount": 0,
  "doi": "10.1007/978-1-0716-5496-5_3",
  "firstAuthor": "Zhang L",
  "firstPublicationDate": "2026-09-15",
  "fullTextUrl": "https://doi.org/10.1007/978-1-0716-5496-5_3",
  "hasPdf": false,
  "inEPMC": false,
  "isOpenAccess": false,
  "issn": "1064-3745",
  "issue": null,
  "journalAbbreviation": "Methods Mol Biol",
  "journalTitle": "Methods in molecular biology (Clifton, N.J.)",
  "keywords": "CRISPR/Cas12a | RT-RPA | Chikungunya",
  "language": "eng",
  "meshTerms": "CRISPR-Cas Systems | Chikungunya virus | Humans",
  "page": 1,
  "pageInfo": "31-44",
  "pmcid": null,
  "pmid": "42734786",
  "publicationTypes": "Journal Article",
  "pubYear": 2027,
  "query": "crispr",
  "scrapedAt": "2026-09-18T09:17:19.446Z",
  "source": "MED",
  "title": "RT-RPA-Assisted CRISPR/Cas12a-Based Isothermal Detection of Chikungunya Virus.",
  "volume": "3067"
}

How to use

Option A — by topic

{
  "maxItems": 1000,
  "maxPagesPerSearch": 4,
  "searchQueries": [
    "crispr"
  ]
}

1. Open the Actor and fill in the first field.
2. Set the page limit and Max items to bound the run.
3. Click Start, then export from the Output tab.

Option B — open access, bounded by date

{
  "includeAbstract": false,
  "maxItems": 5000,
  "maxPagesPerSearch": 10,
  "openAccessOnly": true,
  "searchQueries": [
    "(gene therapy) AND (FIRST_PDATE:[2024 TO 2026])"
  ]
}

Everything in the first field is processed independently, so you can batch several targets into one run and split them apart afterwards.

Input parameters

Parameter	Type	Default	Description
searchQueries	array	–	Europe PMC queries to run, e.
openAccessOnly	boolean	false	Restrict to articles whose full text is open access and reusable.
includeAbstract	boolean	true	Include the full abstract.
maxPagesPerSearch	integer	4	How many result pages to walk for each search.
maxItems	integer	500	Stop after this many articles.
maxConcurrency	integer	2	Parallel requests.
proxyConfiguration	object	{"useApifyProxy": true}	Proxy used to fetch pages.

Tips for best results

• Europe PMC query syntax works as-is: crispr, AUTH:"Doudna J", JOURNAL:"Nature" all run.
• Add AND (FIRST_PDATE:[2024 TO 2026]) to a query to bound it by date.
• Open access only appends the right filter for you when you intend to reuse full text.
• The API returns up to 1,000 records per request, so exports need few calls.
• Paging uses a cursor, so a run can walk far past the first thousand hits.
• abstractText is full text, so exports get large — cap results if you only need metadata.
• meshTerms and keywords are pipe-separated so the columns survive a CSV round trip.
• Europe PMC publishes Y/N flags for access status; the Actor converts them to real booleans.
• Preprints appear with source PPR and usually carry no PMID.
• Pair with the PubMed and Crossref scrapers to widen or cross-check coverage.

Integrations

Send results straight into the tools you already use: Google Sheets, Slack, Zapier, Make, Airtable or any Webhook. You can also schedule the Actor to run hourly, daily or weekly and have each run append to the same dataset, which is how you build a price or availability history rather than a one-off snapshot.

API usage

Run the Actor and collect results from any language. Replace <YOUR_TOKEN> with your Apify API token.

cURL

curl -X POST "https://api.apify.com/v2/acts/logiover~europepmc-literature-scraper/run-sync-get-dataset-items?token=<YOUR_TOKEN>" \
  -H "Content-Type: application/json" \
  -d '{"maxItems": 1000, "maxPagesPerSearch": 4, "searchQueries": ["crispr"]}'

Node.js

import { ApifyClient } from 'apify-client';

const client = new ApifyClient({ token: '<YOUR_TOKEN>' });
const run = await client.actor('logiover/europepmc-literature-scraper').call({"maxItems": 1000, "maxPagesPerSearch": 4, "searchQueries": ["crispr"]});
const { items } = await client.dataset(run.defaultDatasetId).listItems();
console.log(items);

Python

from apify_client import ApifyClient

client = ApifyClient('<YOUR_TOKEN>')
run = client.actor('logiover/europepmc-literature-scraper').call(run_input={"maxItems": 1000, "maxPagesPerSearch": 4, "searchQueries": ["crispr"]})
for item in client.dataset(run['defaultDatasetId']).iterate_items():
    print(item)

Use with AI agents (MCP)

This Actor is available through the Apify MCP server, so an AI agent can call it as a tool. Point your agent at https://mcp.apify.com and it can run the Europe PMC Scraper on demand — for example: "Pull the first 500 articles from Europe PMC and summarise what you find." The agent receives the same structured rows you would get from the UI.

FAQ

Do I need a Europe PMC account or API key?

No. The Actor reads publicly available data only. There is nothing to authenticate and no credentials to rotate.

How many articles can I get in one run?

As many as the source exposes. Raise the page limit and Max items together; the run stops at whichever limit it reaches first.

Why did I get fewer rows than I asked for?

The source ran out of articles. That is normal for narrow searches — broaden the query or add more targets to one run.

Are results de-duplicated?

Yes. Each article is emitted once per run, even when it appears on several pages, so you are never billed twice for the same record.

Why are some fields empty?

Europe PMC does not publish every attribute for every article. Empty means the source did not supply it, not that extraction failed.

What export formats are supported?

JSON, CSV, Excel, HTML and RSS from the Output tab, plus the Apify API and any integration you connect.

How fast is it?

It is pure HTTP with no browser, so a page of results typically takes a second or two. Raise Max concurrency carefully — the source rate-limits aggressive crawling.

Can I schedule it?

Yes. Use the Apify scheduler to run it on any interval and append each run to the same dataset for time-series analysis.

Does it work behind a proxy?

It uses Apify Proxy automatically. You can switch groups or supply your own proxies in Proxy configuration.

How often does the data change?

Europe PMC updates continuously. Re-run whenever you need current data; the Actor always reads the live source, never a cache.

Is the output schema stable?

Yes. Field names and types are fixed, so downstream pipelines will not break between runs.

What if the source changes its format?

Open an issue on the Issues tab and it gets fixed. The Actor is actively maintained.

Is it legal?

This Actor reads only publicly available data from Europe PMC — the same content any visitor or client sees without logging in. It does not bypass authentication, does not collect private data and does not attempt to defeat access controls. You are responsible for how you use the output: respect the source's terms of service, applicable copyright, and data-protection law such as GDPR where personal data is involved. Scraping public data is generally lawful in the EU and the US, but the responsibility for the downstream use of that data sits with you.

Related scrapers

• PubMed Scraper — The MEDLINE subset
• Crossref Scraper — DOI and citation metadata
• arXiv Scraper — Preprint metadata
• OpenAlex Scraper — Works, authors and institutions