# Europe PMC & PubMed Literature Metadata Exporter (`archive-scout-labs/europe-pmc-publications-exporter`) Actor

Search Europe PMC and PubMed literature by topic, author, journal, date, DOI, PMID, open access, or citation count. Export abstracts, structured authors, affiliations, MeSH terms, grants, citations, and full-text links.

- **URL**: https://apify.com/archive-scout-labs/europe-pmc-publications-exporter.md
- **Developed by:** [Archive Scout Labs](https://apify.com/archive-scout-labs) (community)
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

from $0.10 / 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.

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 & PubMed Literature Metadata Exporter

Search life-science and biomedical literature through the official Europe PMC REST API. Turn a topic, author, journal, DOI, PMID, or advanced Europe PMC query into clean dataset rows with abstracts, structured authors, affiliations, citations, MeSH terms, grants, and full-text links.

This HTTP-only Apify Actor needs no customer login, cookie, proxy, or third-party API subscription. It returns metadata, not downloaded article files.

### Quick start

1. Enter a literature query.
2. Choose relevance, most cited, or newest first.
3. Keep the result limit small for the first run.
4. Click **Start** and export the dataset as JSON, CSV, Excel, XML, RSS, or HTML.

```json
{
  "query": "OPEN_ACCESS:Y AND machine learning",
  "sort": "P_PDATE_D desc",
  "expandSynonyms": false,
  "maxItems": 25
}
```

### Query examples

| Goal | Query |
|---|---|
| Topic search | `cancer immunotherapy` |
| Author search | `AUTH:"Jane Smith"` |
| Journal search | `JOURNAL:"Nature Medicine"` |
| Exact DOI | `DOI:10.1038/s41591-024-00000-0` |
| Open-access papers | `OPEN_ACCESS:Y AND malaria` |
| Papers with abstracts | `HAS_ABSTRACT:Y AND microbiome` |

Europe PMC supports Boolean operators, field qualifiers, identifiers, and date expressions. Use focused queries to reduce noise and cost.

### What each result includes

Each publication row can include:

- PMID, PMCID, DOI, source identifier, and Europe PMC URL
- title, abstract, publication types, journal, volume, issue, pages, and dates
- structured authors, ORCID-style identifiers when supplied, and affiliations
- citation count, open-access and full-text availability flags
- keywords, MeSH headings, grants, and full-text links when supplied by Europe PMC
- a retrieval timestamp for repeatable monitoring workflows

Fields remain `null` when the source does not provide them. The Actor does not invent missing metadata.

### Useful workflows

- Literature-review discovery and screening exports
- PubMed, PMCID, and DOI enrichment
- New-publication monitoring by topic, author, institution, or journal
- Open-access evidence discovery
- Citation, grant, affiliation, and research-landscape analysis
- Scheduled feeds for spreadsheets, databases, webhooks, MCP clients, and AI workflows

### Reliability and billing design

- Uses Europe PMC's `core` result type for richer metadata.
- Supports cursor pagination without duplicating records within a run.
- Bounds default and maximum result counts to prevent accidental runaway jobs.
- Retries temporary rate limits and server errors with exponential backoff.
- Fails loudly on unexpected source response shapes instead of returning a misleading empty success.
- Charges only for successfully written dataset rows when pay-per-result pricing is enabled.
- Stops cleanly when an Apify maximum-charge limit is reached.

### Data source and limitations

Source documentation: https://dev.europepmc.org/RestfulWebService

Europe PMC aggregates records from sources that include PubMed and PubMed Central. Coverage, citation counts, update timing, and field completeness can differ from Scopus, Web of Science, a publisher's site, or the final article. Full-text links indicate source-reported availability; this Actor does not grant access rights or download papers.

This independent community Actor is not affiliated with or endorsed by Europe PMC, EMBL-EBI, PubMed, PMC, or the U.S. National Library of Medicine. Users remain responsible for interpreting and using the data lawfully.

# Actor input Schema

## `query` (type: `string`):

A topic, author, journal, identifier, or Europe PMC query expression. Examples: cancer immunotherapy; AUTH:"Jane Smith"; OPEN\_ACCESS:Y AND malaria.

## `sort` (type: `string`):

Choose relevance, citation count, or newest publication date.

## `expandSynonyms` (type: `boolean`):

Expand query terms with Europe PMC's MeSH and UniProt synonym lists.

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

Maximum number of publication rows to write. Start small, then increase after checking the query.

## Actor input object example

```json
{
  "query": "OPEN_ACCESS:Y AND machine learning",
  "sort": "relevance",
  "expandSynonyms": false,
  "maxItems": 25
}
```

# Actor output Schema

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

Default dataset containing successful source records.

# 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 = {};

// Run the Actor and wait for it to finish
const run = await client.actor("archive-scout-labs/europe-pmc-publications-exporter").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 = {}

# Run the Actor and wait for it to finish
run = client.actor("archive-scout-labs/europe-pmc-publications-exporter").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 '{}' |
apify call archive-scout-labs/europe-pmc-publications-exporter --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "type": "http",
            "url": "https://mcp.apify.com/?tools=fetch-actor-details,archive-scout-labs/europe-pmc-publications-exporter"
        }
    }
}
```

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/jtacL4wqd6Vh64wh5/builds/YDdE3go9078gfRidL/openapi.json