# PubMed Scraper (`alleserojje/pubmed-scraper`) Actor

Search PubMed (35M+ biomedical papers) and export structured records — title, authors, abstract, journal, year, DOI, MeSH terms, publication types — via the official NCBI E-utilities API. No key, no anti-bot. Pay per paper.

- **URL**: https://apify.com/alleserojje/pubmed-scraper.md
- **Developed by:** [Pedro Resende](https://apify.com/alleserojje) (community)
- **Categories:** Education, AI, Agents
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

from $1.00 / 1,000 paper scrapeds

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?

Actors are web data automations that power AI and operations. They run on the Apify platform to scrape websites, process data, connect APIs, and automate workflows.
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.
Actors are written with capital "A".

## 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.
The best way to integrate Actors is as follows.

- **AI agents and MCP clients** — the [Apify MCP server](https://docs.apify.com/integrations/mcp.md) at `https://mcp.apify.com` (remote, streamable HTTP, OAuth on first use).
- **Agentic workflows and local Actor development** — [Agent Skills](https://apify.com/.well-known/agent-skills/index.json) with the [Apify CLI](https://docs.apify.com/cli/docs.md): `npm install -g apify-cli`, then `apify login`.
- **JavaScript/TypeScript projects** — the official [JS/TS client](https://docs.apify.com/api/client/js/docs.md): `npm install apify-client`.
- **Python projects** — the official [Python client](https://docs.apify.com/api/client/python/docs.md): `pip install apify-client`.
- **Any other language** — the [REST API](https://docs.apify.com/api/v2.md).

For usage examples, see the [API](#api) section below.

For more details, see Apify documentation as [Markdown index](https://docs.apify.com/llms.txt) and [Markdown full-text](https://docs.apify.com/llms-full.txt).

# README

## PubMed Scraper

**PubMed Scraper** searches PubMed (35M+ biomedical papers) and returns rich, structured records — PMID, title, authors, abstract, journal, year, DOI, MeSH terms and publication types — via the official NCBI E-utilities API. No API key, no anti-bot, no rental. Pay only per paper.

### What this PubMed scraper does

- **Search** PubMed by keyword using the full PubMed query syntax (`AND`/`OR`/`NOT`, field tags like `[tiab]`, `[MeSH]`, `author:`, `journal:`).
- **Fetch** specific papers by PubMed ID (PMID), e.g. `32838224`.
- **Filter** by publication year range.
- **Sort** by relevance, publication date, author, or journal, and page with `start`.
- **Export** title, full abstract, author list, journal, year, DOI, MeSH terms and publication types per paper.
- Great for **literature review**, **systematic reviews**, **biomedical datasets**, and feeding papers into AI/LLM pipelines.

### Input

| Field | Description |
|---|---|
| `query` | Search terms (full PubMed syntax). |
| `idList` | Fetch specific papers by PMID. |
| `maxResults` | Max papers to return (1–500). |
| `start` | Pagination offset (0-based). |
| `sortBy` | `relevance`, `pub_date`, `author`, or `journal`. |
| `minYear` / `maxYear` | Restrict publication year range. |
| `includeAbstract` | Fetch full abstract text (default true). |

### Output

Each dataset item includes `pmid`, `title`, `abstract`, `authors[]`, `journal`, `journalAbbrev`, `year`, `month`, `day`, `pubDate`, `doi`, `pubTypes[]`, `meshTerms[]`, `pmidUrl` and `scrapedAt`.

### Pricing

**Pay per event:** billed once per paper returned. An aborted run only pays for what it delivered. No monthly rental.

> Note: this Actor returns PubMed metadata via the official NCBI E-utilities API — no scraping of third-party PDF hosts.

# Actor input Schema

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

Search terms. Supports full PubMed query syntax: "covid-19 vaccine efficacy", author:smith, journal:nature, AND/OR/NOT, field tags like \[tiab], \[MeSH].

## `idList` (type: `array`):

Fetch specific papers by PubMed ID, e.g. 32838224.

## `maxResults` (type: `integer`):

Max papers to return (1-500).

## `start` (type: `integer`):

Pagination offset (0-based).

## `sortBy` (type: `string`):

Order results by relevance, publication date, author, or journal.

## `minYear` (type: `integer`):

Optional. Restrict to papers published in or after this year.

## `maxYear` (type: `integer`):

Optional. Restrict to papers published in or before this year.

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

Fetch full abstract text for each paper (adds one extra request per 200 papers).

## `proxy` (type: `object`):

Not required — NCBI E-utilities is open. Datacenter proxy available if you want it.

## Actor input object example

```json
{
  "query": "cancer immunotherapy checkpoint",
  "idList": [
    "32838224"
  ],
  "maxResults": 20,
  "start": 0,
  "sortBy": "relevance",
  "includeAbstract": true,
  "proxy": {
    "useApifyProxy": false
  }
}
```

# Actor output Schema

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

No description

# 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 = {
    "query": "diabetes AND metformin",
    "idList": [
        "32838224"
    ]
};

// Run the Actor and wait for it to finish
const run = await client.actor("alleserojje/pubmed-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 = {
    "query": "diabetes AND metformin",
    "idList": ["32838224"],
}

# Run the Actor and wait for it to finish
run = client.actor("alleserojje/pubmed-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 '{
  "query": "diabetes AND metformin",
  "idList": [
    "32838224"
  ]
}' |
apify call alleserojje/pubmed-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "type": "http",
            "url": "https://mcp.apify.com/?tools=fetch-actor-details,alleserojje/pubmed-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/FFbdw3rBfRPaoyrt4/builds/yzdeZnQVC12n4DszJ/openapi.json