# PubMed Research Scraper - Papers, Abstracts & Authors (`thirdwatch/pubmed-research-scraper`) Actor

Search PubMed through the official NCBI E-utilities API. Export PMIDs, DOIs, titles, abstracts, authors, affiliations, journals, publication types, MeSH terms, and dates.

- **URL**: https://apify.com/thirdwatch/pubmed-research-scraper.md
- **Developed by:** [Thirdwatch](https://apify.com/thirdwatch) (community)
- **Categories:** Developer tools
- **Features:** Limited permissions
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

from $0.70 / 1,000 pubmed articles

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

## PubMed Research Scraper - Papers, Abstracts & Authors

> **Thirdwatch portfolio:** 8,800+ users across 140+ public Actors, 2M+ records delivered, >95% run success. [Explore all Thirdwatch Actors](https://apify.com/thirdwatch).

> Search PubMed literature — titles, authors, abstracts, journals, and publication dates from the NIH index.

### What you get

Search PubMed literature — titles, authors, abstracts, journals, and publication dates from the NIH index.

### Why use this PubMed Research scraper

- **Full citation metadata** — title, authors, abstract, journal, date, and PubMed links.
- **NIH's public index** — stable, free, no key required.
- **Biomedical coverage** — the canonical literature source for life sciences.

### Scrape PubMed Research data in minutes

```json
{
  "queries": [
    "covid-19 vaccine"
  ]
}
```

```json
{
  "queries": [
    "CRISPR gene editing"
  ]
}
```

### Input parameters

| Parameter | Required | Description |
|---|---:|---|
| `queries` | Yes | PubMed search expressions. NCBI field tags such as \[Title], \[Author], and \[MeSH Terms] are supported. Default: `['artificial intelligence in medicine']`. |
| `publicationFrom` | No | Optional start date in YYYY-MM-DD format. Applied to PubMed publication dates. |
| `publicationTo` | No | Optional end date in YYYY-MM-DD format. Applied to PubMed publication dates. |
| `sort` | No | Order returned by the official PubMed search endpoint. One of: pub date, relevance, first author, journal name. Default: `pub date`. |
| `maxResultsPerQuery` | No | Stop after this many unique PubMed articles for each query. Default: `100`. |

### Output fields

- `pmid`
- `doi`
- `pmc_id`
- `title`
- `abstract`
- `authors`
- `affiliations`
- `journal`
- `journal_abbreviation`
- `issn`
- `publication_date`
- `volume`
- `issue`
- `pages`
- `language`
- `publication_types`
- `mesh_terms`
- `keywords`
- `pubmed_url`
- `query`
- `source`
- `email`
- `tool`

#### Example result

```json
{
  "pmid": "42641684",
  "doi": "10.1016/j.annonc.2026.07.001",
  "pmc_id": null,
  "title": "Thymic Radiation is Associated with Worse Outcomes in Patients with NSCLC.",
  "abstract": "BACKGROUND: Emerging evidence indicates the functional importance of the thymus in adult health and may influence oncolo…",
  "authors": [
    "V Prudente",
    "S Bernatz",
    "S Pai",
    "…"
  ],
  "affiliations": [
    "Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USA; Department of Radiation Oncology, Mass General Brigham Cancer Institute, Harvard Medical School, Boston, MA, USA; Radiology and Nuclear Medicine, CARIM & GROW, Maastricht University, Maastricht, Netherlands.",
    "Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA.",
    "Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.",
    "…"
  ],
  "journal": "Annals of oncology : official journal of the European Society for Medical Oncology",
  "journal_abbreviation": "Ann Oncol",
  "issn": "1569-8041",
  "publication_date": "2026-12-31",
  "volume": null,
  "issue": null,
  "pages": null,
  "language": "eng",
  "publication_types": [
    "Journal Article"
  ],
  "mesh_terms": [],
  "keywords": [
    "Artificial Intelligence",
    "Organ of Interest",
    "Radiation Oncology",
    "Radiotherapy",
    "Thymic Health",
    "| Thymus"
  ],
  "pubmed_url": "https://pubmed.ncbi.nlm.nih.gov/42641684/",
  "query": "artificial intelligence in medicine",
  "source": "PubMed"
}
```

### Common use cases

- Monitor new papers in a therapeutic area
- Build systematic-review datasets
- Feed evidence-mining pipelines
- Track lab and author output

### Compared to alternatives

- **vs other PubMed Research scrapers on the Store** — pay-per-result billing means empty or failed searches cost nothing; you are not charged for a run that returns zero rows.
- **vs building your own** — no proxy management, markup-change maintenance, or infrastructure to run; paste inputs and consume the dataset.

### Limitations

- Abstracts included; full text lives at the publisher, not in the dataset.
- PubMed indexing lags publication by days for some journals.
- `mesh_terms` and `doi` are sometimes empty when PubMed has not yet indexed them for an article.
- Bound large queries with `maxResultsPerQuery` to stay within API limits.

### FAQ

**Do I need an account or cookies?**

No — the Actor reads public data only. There is no login to configure and no account to risk.

**What happens when a search returns nothing?**

The run completes with zero (or an explicit error) rows. Per-result billing means you are not charged for empty output.

**Can I run it on a schedule?**

Yes — attach an Apify schedule or use the saved tasks to re-run the same inputs daily or weekly.

### Related guides and Actors

- [Analyze Pubmed Papers With Python](https://thirdwatch.dev/blog/analyze-pubmed-papers-with-python)
- [Build Pubmed Literature Review Dataset](https://thirdwatch.dev/blog/build-pubmed-literature-review-dataset)
- [Find Clinical Research Authors And Affiliations](https://thirdwatch.dev/blog/find-clinical-research-authors-and-affiliations)
- [Clinical Trials Scraper](https://apify.com/thirdwatch/clinical-trials-gov-scraper?fpr=9m2cd6)

Last verified: 2026-09

More scrapers at [thirdwatch.dev](https://thirdwatch.dev).

# Actor input Schema

## `queries` (type: `array`):

PubMed search expressions. NCBI field tags such as \[Title], \[Author], and \[MeSH Terms] are supported.

## `publicationFrom` (type: `string`):

Optional start date in YYYY-MM-DD format. Applied to PubMed publication dates.

## `publicationTo` (type: `string`):

Optional end date in YYYY-MM-DD format. Applied to PubMed publication dates.

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

Order returned by the official PubMed search endpoint.

## `maxResultsPerQuery` (type: `integer`):

Stop after this many unique PubMed articles for each query.

## Actor input object example

```json
{
  "queries": [
    "artificial intelligence in medicine"
  ],
  "sort": "pub date",
  "maxResultsPerQuery": 100
}
```

# 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 = {
    "queries": [
        "artificial intelligence in medicine"
    ],
    "sort": "pub date",
    "maxResultsPerQuery": 100
};

// Run the Actor and wait for it to finish
const run = await client.actor("thirdwatch/pubmed-research-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 = {
    "queries": ["artificial intelligence in medicine"],
    "sort": "pub date",
    "maxResultsPerQuery": 100,
}

# Run the Actor and wait for it to finish
run = client.actor("thirdwatch/pubmed-research-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 '{
  "queries": [
    "artificial intelligence in medicine"
  ],
  "sort": "pub date",
  "maxResultsPerQuery": 100
}' |
apify call thirdwatch/pubmed-research-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "type": "http",
            "url": "https://mcp.apify.com/?tools=fetch-actor-details,thirdwatch/pubmed-research-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/fJpY1kJls1N8gd9jn/builds/j50k27zaNTKXuazNX/openapi.json