# Europe PMC Scraper - Papers, Abstracts & Citations (`logiover/europepmc-literature-scraper`) Actor

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.

- **URL**: https://apify.com/logiover/europepmc-literature-scraper.md
- **Developed by:** [Logiover](https://apify.com/logiover) (community)
- **Categories:** Developer tools
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

from $3.50 / 1,000 results

This Actor is paid per event. You are not charged for the Apify platform usage, but only a fixed price for specific events.
Since this Actor supports Apify Store discounts, the price gets lower the higher subscription plan you have.

Learn more: https://docs.apify.com/actors/running/actors-in-store.md#pay-per-event

## What's an Apify Actor?

An Actor is a serverless cloud program that runs on the Apify platform. It has two run modes.
In Batch mode, an Actor accepts a well-defined JSON input, performs an action which can take anything from a few seconds to a few hours,
and optionally produces a well-defined JSON output, datasets with results, or files in key-value store.
In Standby mode, an Actor provides a web server which can be used as a website, API, or an MCP server.

Apify vocabulary and the platform model are defined once, in the agent quickstart at https://apify.com/agents.md.

## How to integrate an Actor?

If asked about integration, you help developers integrate Actors into their projects.
You adapt to their stack and deliver integrations that are safe, well-documented, and production-ready.

Do not guess an integration path. Every one of them is in the agent quickstart at https://apify.com/agents.md: the Apify MCP server, Agent Skills with the Apify CLI, the JavaScript and Python clients, the REST API, and the account-free path for an agent with no human to sign in. It also carries the rule on stating cost before the first paid run.

For examples already wired to this Actor's own input schema, see the [API](#api) section below.

Each client library has reference documentation the quickstart does not restate: [JavaScript/TypeScript](https://docs.apify.com/api/client/js/docs.md) (`npm install apify-client`) and [Python](https://docs.apify.com/api/client/python/docs.md) (`pip install apify-client`).

# README

## Europe PMC Scraper - Papers, Abstracts & Citations

![Apify Actor](https://img.shields.io/badge/Apify-Actor-00A67E?logo=apify\&logoColor=white) ![No API key](https://img.shields.io/badge/No%20API%20key-required-2ea44f) ![Pay per result](https://img.shields.io/badge/Pricing-Pay%20per%20result-1C7ED6) ![Export](https://img.shields.io/badge/Export-JSON%20%7C%20CSV%20%7C%20Excel-F59E0B)

**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.**

***

### 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

```json
{
  "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

```json
{
  "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

```json
{
  "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**

```bash
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**

```javascript
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**

```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](https://apify.com/logiover/pubmed-scraper) — The MEDLINE subset
- [Crossref Scraper](https://apify.com/logiover/crossref-scraper) — DOI and citation metadata
- [arXiv Scraper](https://apify.com/logiover/arxiv-paper-scraper) — Preprint metadata
- [OpenAlex Scraper](https://apify.com/logiover/openalex-scraper) — Works, authors and institutions

# Actor input Schema

## `searchQueries` (type: `array`):

Europe PMC queries to run, e.g. crispr, AUTH:"Doudna J". Each query is crawled independently.

## `openAccessOnly` (type: `boolean`):

Restrict to articles whose full text is open access and reusable.

## `includeAbstract` (type: `boolean`):

Include the full abstract. Turn off for a much smaller export when you only need citation metadata.

## `maxPagesPerSearch` (type: `integer`):

How many result pages to walk for each search. Set 0 for no limit.

## `maxItems` (type: `integer`):

Stop after this many articles. Set 0 for no limit.

## `maxConcurrency` (type: `integer`):

Parallel requests. Lower this if the source rate-limits you.

## `proxyConfiguration` (type: `object`):

Proxy used to fetch pages. Defaults to Apify Proxy (automatic). You usually do not need to change this.

## Actor input object example

```json
{
  "searchQueries": [
    "crispr"
  ],
  "openAccessOnly": false,
  "includeAbstract": true,
  "maxPagesPerSearch": 4,
  "maxItems": 500,
  "maxConcurrency": 2,
  "proxyConfiguration": {
    "useApifyProxy": true
  }
}
```

# Actor output Schema

## `results` (type: `string`):

All articles extracted in this run.

# API

You can run this Actor programmatically using our API. Below are code examples in JavaScript, Python, and CLI, as well as the OpenAPI specification and MCP server setup.

## JavaScript example

```javascript
import { ApifyClient } from 'apify-client';

// Initialize the ApifyClient with your Apify API token
// Replace the '<YOUR_API_TOKEN>' with your token
const client = new ApifyClient({
    token: '<YOUR_API_TOKEN>',
});

// Prepare Actor input
const input = {
    "searchQueries": [
        "crispr"
    ],
    "maxPagesPerSearch": 4,
    "maxItems": 500,
    "maxConcurrency": 2
};

// Run the Actor and wait for it to finish
const run = await client.actor("logiover/europepmc-literature-scraper").call(input);

// Fetch and print Actor results from the run's dataset (if any)
console.log('Results from dataset');
console.log(`💾 Check your data here: https://console.apify.com/storage/datasets/${run.defaultDatasetId}`);
const { items } = await client.dataset(run.defaultDatasetId).listItems();
items.forEach((item) => {
    console.dir(item);
});

// 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/js/docs

```

## Python example

```python
from apify_client import ApifyClient

# Initialize the ApifyClient with your Apify API token
# Replace '<YOUR_API_TOKEN>' with your token.
client = ApifyClient("<YOUR_API_TOKEN>")

# Prepare the Actor input
run_input = {
    "searchQueries": ["crispr"],
    "maxPagesPerSearch": 4,
    "maxItems": 500,
    "maxConcurrency": 2,
}

# Run the Actor and wait for it to finish
run = client.actor("logiover/europepmc-literature-scraper").call(run_input=run_input)

# Fetch and print Actor results from the run's dataset (if there are any)
print(f"💾 Check your data here: https://console.apify.com/storage/datasets/{run.default_dataset_id}")
for item in client.dataset(run.default_dataset_id).iterate_items():
    print(item)

# 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/python/docs/quick-start

```

## CLI example

```bash
echo '{
  "searchQueries": [
    "crispr"
  ],
  "maxPagesPerSearch": 4,
  "maxItems": 500,
  "maxConcurrency": 2
}' |
apify call logiover/europepmc-literature-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "type": "http",
            "url": "https://mcp.apify.com/?tools=fetch-actor-details,logiover/europepmc-literature-scraper"
        }
    }
}
```

The hosted server signs you in with OAuth on first connect, so no API token belongs in this config. Clients without OAuth support can send an `Authorization: Bearer <APIFY_API_TOKEN>` header instead, using a token from API & Integrations in Apify Console (https://console.apify.com/settings/integrations).

## OpenAPI specification

Download the OpenAPI definition: https://api.apify.com/v2/actors/j1cc66ZUhXgqkWsK9/builds/DqvgsfIIqEeJPGuLW/openapi.json