# PubMed Scraper - Biomedical Articles & Metadata (`scrapesage/pubmed-scraper`) Actor

Scrape PubMed biomedical articles by search query or PMID from the NCBI E-utilities API: title, journal, authors, date, DOI, volume/issue/pages, ISSN and publication types. No key, no browser.

- **URL**: https://apify.com/scrapesage/pubmed-scraper.md
- **Developed by:** [Scrape Sage](https://apify.com/scrapesage) (community)
- **Categories:** Agents, Integrations, Other
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

from $1.10 / 1,000 article scrapeds

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/platform/actors/running/actors-in-store#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 - Biomedical Articles & Metadata

Search **PubMed** and get clean, structured rows for every biomedical article: **title**, **journal**,
**authors**, **publication date**, **DOI**, volume/issue/pages, **ISSN** and publication types. Search by
keyword (or PubMed field tags), or fetch exact articles by PMID. Built on the official NCBI E-utilities
API - no key, no browser.

### What you get per article

| Field | Meaning |
|---|---|
| `title` / `journal` / `journalAbbrev` | Article title and journal (full + abbreviated) |
| `authors` / `lastAuthor` | Author list and the senior (last) author |
| `pubDate` / `epubDate` | Print and electronic publication dates |
| `doi` / `pmcId` / `pmid` | DOI, PubMed Central ID, PubMed ID |
| `volume` / `issue` / `pages` / `issn` | Citation details |
| `pubTypes` / `pubmedUrl` / `doiUrl` | Publication types and direct links |

### Input

```json
{ "searchQueries": ["cancer immunotherapy"], "maxItemsPerQuery": 100, "sortBy": "date" }
```

- **Search queries** - one per line. Plain terms work, and so do PubMed field tags:
  `cancer[Title]`, `Smith J[Author]`, `2024[pdat]`, `clinical trial[pt]`.
- **PMIDs** - or fetch specific articles by PubMed ID.
- **Import from a file** - paste a whole list, or link a public `.txt`/`.csv`, a Google Sheet/Drive link,
  or an Apify key-value-store record.
- **Sort by** relevance, publication date, or first author. **Max articles per query / total** bound the run.
- **Output fields** - tick only the columns you want.

Leave everything empty and the run returns a small free sample so you can see the shape first.

### Reliability

Reads the official [NCBI E-utilities](https://www.ncbi.nlm.nih.gov/books/NBK25501/) API - public JSON, no
key, no proxy, no anti-bot. The actor paces requests to stay within NCBI's 3-requests-per-second guidance.
A run that returns nothing bills **$0**.

### Honest limits

- **Citation metadata, not full text.** You get the article's bibliographic record (title, journal,
  authors, DOI, IDs); the full text lives at the publisher or PubMed Central via the links.
- **`pmcId` is present only for articles indexed in PubMed Central**; `doi` and `epubDate` follow what the
  record publishes. These vary by article, not by extraction.

### Pricing

**$0.002 per article** on the FREE tier (tiered pricing lowers it with volume). Only articles actually
saved are billed; an empty run costs nothing.

### Output views

- **Articles** - title, journal, authors, date, DOI, PMID and the PubMed link.

### Use with AI assistants (MCP)

Available through the [Apify MCP server](https://docs.apify.com/platform/integrations/mcp) - an agent can
pull the latest literature on a condition or drug (with DOIs) for a review or evidence-synthesis pipeline.

### Agent-ready: autonomous payments (x402 & Skyfire)

This actor is **agent-ready** - AI agents can discover it, run it, and **pay for it autonomously**, with no Apify account and no human in the loop. It uses [pay-per-event](https://docs.apify.com/platform/actors/publishing/monetize/pay-per-event) pricing and [limited permissions](https://docs.apify.com/platform/actors/development/permissions), so it qualifies for Apify's agentic-payment standards:

- **[x402](https://docs.apify.com/platform/integrations/x402)** - an open, HTTP-native payment protocol. Agents pay per run in USDC on the Base network directly through the [Apify MCP server](https://docs.apify.com/platform/integrations/mcp) - no account, no API key.
- **[Skyfire](https://docs.apify.com/platform/integrations/skyfire)** - agent-to-service payments for fully autonomous AI-agent workflows.

Building an AI agent, MCP tool, or autonomous data pipeline? This scraper is ready to plug in and pay as it goes.

# Actor input Schema

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

What to search PubMed for, one per line - e.g. <code>crispr</code>, <code>alzheimer immunotherapy</code>. PubMed field tags work too (<code>cancer\[Title]</code>, <code>Smith J\[Author]</code>, <code>2024\[pdat]</code>). <b>Leave empty and the run returns a small free sample.</b>

## `pmids` (type: `array`):

Fetch specific articles by PubMed ID (e.g. <code>38000000</code>). When set, articles are fetched by ID.

## `searchQueriesFromFile` (type: `string`):

Bulk-load search queries. Either <b>paste the whole list</b> (one per line), or give <b>a single link</b> to a public <code>.txt</code>/<code>.csv</code>, a Google Sheet/Drive link, or an Apify key-value-store record. A file that cannot be read says so and charges nothing.

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

How to order search results.

## `maxItemsPerQuery` (type: `integer`):

How many articles to collect for each search query.

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

Overall cap across all queries. You are only charged for articles actually saved.

## `outputFields` (type: `array`):

Pick the fields you want and every record is trimmed to exactly those - handy for lean CSV/Sheets exports.

## Actor input object example

```json
{
  "searchQueries": [
    "crispr"
  ],
  "sortBy": "relevance",
  "maxItemsPerQuery": 50,
  "maxItems": 1000
}
```

# Actor output Schema

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

Each scraped record - PubMed articles - as a JSON item in the default dataset.

# 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"
    ],
    "searchQueriesFromFile": ""
};

// Run the Actor and wait for it to finish
const run = await client.actor("scrapesage/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 = {
    "searchQueries": ["crispr"],
    "searchQueriesFromFile": "",
}

# Run the Actor and wait for it to finish
run = client.actor("scrapesage/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 '{
  "searchQueries": [
    "crispr"
  ],
  "searchQueriesFromFile": ""
}' |
apify call scrapesage/pubmed-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "type": "http",
            "url": "https://mcp.apify.com/?tools=fetch-actor-details,scrapesage/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/zwZvSECfArELaKKhL/builds/IydKiBE4S3IuNKkb2/openapi.json