# PubMed Scraper — Bulk Biomedical Papers, Abstracts & Metadata (`hipersoft/pubmed-scraper`) Actor

Bulk-scrape PubMed's 35M+ biomedical articles: title, abstract, authors, journal, publication date, DOI, PMC ID, MeSH terms and keywords. Full PubMed query syntax, date filters, thousands of results per run. Powered by NCBI E-utilities. No login, no API key.

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

## Pricing

from $0.0004 / article scraped

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/platform/actors/running/actors-in-store#pay-per-event

## What's an Apify Actor?

Actors are a software tools running on the Apify platform, for all kinds of web data extraction and automation use cases.
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.

In JavaScript/TypeScript projects, use official [JavaScript/TypeScript client](https://docs.apify.com/api/client/js/docs.md):

```bash
npm install apify-client
```

In Python projects, use official [Python client library](https://docs.apify.com/api/client/python/docs.md):

```bash
pip install apify-client
```

In shell scripts, use [Apify CLI](https://docs.apify.com/cli/docs.md):

````bash
# MacOS / Linux
curl -fsSL https://apify.com/install-cli.sh | bash
# Windows
irm https://apify.com/install-cli.ps1 | iex
```bash

In AI frameworks, you might use the [Apify MCP server](https://docs.apify.com/integrations/mcp.md).

If your project is in a different language, use 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 — Bulk Biomedical Papers, Abstracts & Metadata

Bulk-scrape biomedical literature from **PubMed** — the U.S. National Library of Medicine's index of **35M+ articles**. Get titles, **full abstracts**, authors, journals, publication dates, DOIs, PMC IDs, MeSH terms and keywords for every matching paper. Full PubMed query syntax, date filters, and thousands of results per run. Powered by the official NCBI E-utilities API. No account, no API key.

### Features

- 🔎 **Full PubMed query syntax** — terms, fields (`[Title]`, `[Author]`, `[MeSH]`), booleans and date ranges
- 📄 **Full abstracts** — complete abstract text for every article that has one
- 👥 **Authors** — full author lists with a count per paper
- 🏷️ **Rich metadata** — journal, publication date, DOI, PMC ID, MeSH terms, keywords, article types
- 📅 **Date filters** — restrict by publication date
- 📊 **Bulk & history-paginated** — one query streams through tens of thousands of results
- ⚡ **Official & reliable** — built on NCBI E-utilities, no scraping tricks, no anti-bot

### What you get

One record per article:

```json
{
  "pmid": "38512345",
  "title": "…",
  "journal": "Nature Medicine",
  "pubYear": 2024,
  "pubDate": "2024 Mar 15",
  "authors": ["Jane A Smith", "…"],
  "authorCount": 8,
  "doi": "10.1038/s41591-024-00000-0",
  "pmcId": "PMC10987654",
  "articleTypes": ["Journal Article"],
  "meshTerms": ["CRISPR-Cas Systems", "Gene Editing"],
  "keywords": ["…"],
  "url": "https://pubmed.ncbi.nlm.nih.gov/38512345/",
  "abstract": "…"
}
````

### Input

```json
{
  "query": "crispr gene editing",
  "dateFrom": "2020",
  "dateTo": "2025",
  "includeAbstract": true,
  "maxResults": 5000
}
```

| Field | Description |
|-------|-------------|
| `query` | Any PubMed search (e.g. `asthma[MeSH] AND treatment`, `covid-19 AND vaccine[Title]`). |
| `dateFrom` / `dateTo` | Publication date range (YYYY/MM/DD or YYYY). |
| `includeAbstract` | Include the full abstract text. |
| `maxResults` | Max articles to return (a broad query can match tens of thousands). |
| `apiKey` | Optional NCBI key to raise the request rate for very large runs. |

### Use cases

- **Systematic & literature reviews** — pull every paper on a topic, with abstracts, in one run
- **Research monitoring** — track new publications in your field by date
- **Biomedical datasets** — build corpora of titles + abstracts for analysis or AI
- **Citation & metadata** — collect DOIs, PMC IDs and MeSH terms at scale

### Pricing

Pay-per-event: a small amount per article scraped. See the **Pricing** tab for current rates.

### FAQ

**Do I need an API key?**
No. This Actor runs on the official NCBI E-utilities API with no account required. You can optionally add an NCBI `apiKey` to raise the request rate for very large runs, but it's not needed for typical use.

**How many articles can I scrape per run?**
Set `maxResults` as high as you need — a single query streams through PubMed's history server, so one broad query can return tens of thousands of articles in a run.

**Is scraping PubMed legal?**
Yes. This Actor uses [PubMed](https://pubmed.ncbi.nlm.nih.gov)'s official NCBI E-utilities API and follows its usage guidance (paced requests, an identified client). It returns openly available metadata as-is and doesn't scrape the site or bypass any anti-bot.

**What format is the output?**
Structured JSON — one record per article — exportable as JSON, CSV or Excel. Each record includes PMID, title, full abstract, authors, journal, publication date, DOI, PMC ID, MeSH terms and keywords.

**Can I filter by date or use PubMed field syntax?**
Yes. The `query` field accepts full PubMed syntax including fields like `[Title]`, `[Author]` and `[MeSH]` plus booleans, and `dateFrom`/`dateTo` restrict results to a publication date range.

### Related Actors

Building a biomedical literature dataset? These other hipersoft scrapers pair well with this one:

- [Europe PMC Scraper](https://apify.com/hipersoft/europepmc-scraper) — life-science papers with full-text links across PubMed, PMC and preprints
- [ClinicalTrials.gov Scraper](https://apify.com/hipersoft/clinicaltrials-scraper) — bulk clinical trial records, sponsors and locations
- [OpenAlex Scraper](https://apify.com/hipersoft/openalex-scraper) — 250M+ scholarly works with citations and abstracts
- [Crossref Scraper](https://apify.com/hipersoft/crossref-scraper) — DOIs, citation counts and metadata from 150M+ works

### Notes

Uses the official NCBI E-utilities API and follows its usage guidance (paced requests, identified client). Returns PubMed's openly-available metadata as-is. PubMed is a service of the U.S. National Library of Medicine; this is an independent tool and is not affiliated with or endorsed by the NLM or NCBI.

# Actor input Schema

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

Any PubMed search query. Supports full syntax: terms, fields (\[Title], \[Author], \[MeSH]), booleans, and date ranges. e.g. "crispr gene editing", "asthma\[MeSH] AND treatment", "covid-19 AND vaccine\[Title]".

## `dateFrom` (type: `string`):

Earliest publication date (YYYY/MM/DD or YYYY). Optional.

## `dateTo` (type: `string`):

Latest publication date (YYYY/MM/DD or YYYY). Optional.

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

Include the full abstract text for each article.

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

Maximum number of articles to return (a broad query can match tens of thousands).

## `apiKey` (type: `string`):

Optional NCBI API key to raise the request rate (3→10/sec) for faster large runs. Not required.

## Actor input object example

```json
{
  "query": "crispr gene editing",
  "includeAbstract": true,
  "maxResults": 1000
}
```

# 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": "crispr gene editing"
};

// Run the Actor and wait for it to finish
const run = await client.actor("hipersoft/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": "crispr gene editing" }

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

# Fetch and print Actor results from the run's dataset (if there are any)
print("💾 Check your data here: https://console.apify.com/storage/datasets/" + run["defaultDatasetId"])
for item in client.dataset(run["defaultDatasetId"]).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": "crispr gene editing"
}' |
apify call hipersoft/pubmed-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "command": "npx",
            "args": [
                "mcp-remote",
                "https://mcp.apify.com/?tools=hipersoft/pubmed-scraper",
                "--header",
                "Authorization: Bearer <YOUR_API_TOKEN>"
            ]
        }
    }
}

```

## OpenAPI specification

```json
{
    "openapi": "3.0.1",
    "info": {
        "title": "PubMed Scraper — Bulk Biomedical Papers, Abstracts & Metadata",
        "description": "Bulk-scrape PubMed's 35M+ biomedical articles: title, abstract, authors, journal, publication date, DOI, PMC ID, MeSH terms and keywords. Full PubMed query syntax, date filters, thousands of results per run. Powered by NCBI E-utilities. No login, no API key.",
        "version": "1.0",
        "x-build-id": "4u8nwuWhi3XEUxJji"
    },
    "servers": [
        {
            "url": "https://api.apify.com/v2"
        }
    ],
    "paths": {
        "/acts/hipersoft~pubmed-scraper/run-sync-get-dataset-items": {
            "post": {
                "operationId": "run-sync-get-dataset-items-hipersoft-pubmed-scraper",
                "x-openai-isConsequential": false,
                "summary": "Executes an Actor, waits for its completion, and returns Actor's dataset items in response.",
                "tags": [
                    "Run Actor"
                ],
                "requestBody": {
                    "required": true,
                    "content": {
                        "application/json": {
                            "schema": {
                                "$ref": "#/components/schemas/inputSchema"
                            }
                        }
                    }
                },
                "parameters": [
                    {
                        "name": "token",
                        "in": "query",
                        "required": true,
                        "schema": {
                            "type": "string"
                        },
                        "description": "Enter your Apify token here"
                    }
                ],
                "responses": {
                    "200": {
                        "description": "OK"
                    }
                }
            }
        },
        "/acts/hipersoft~pubmed-scraper/runs": {
            "post": {
                "operationId": "runs-sync-hipersoft-pubmed-scraper",
                "x-openai-isConsequential": false,
                "summary": "Executes an Actor and returns information about the initiated run in response.",
                "tags": [
                    "Run Actor"
                ],
                "requestBody": {
                    "required": true,
                    "content": {
                        "application/json": {
                            "schema": {
                                "$ref": "#/components/schemas/inputSchema"
                            }
                        }
                    }
                },
                "parameters": [
                    {
                        "name": "token",
                        "in": "query",
                        "required": true,
                        "schema": {
                            "type": "string"
                        },
                        "description": "Enter your Apify token here"
                    }
                ],
                "responses": {
                    "200": {
                        "description": "OK",
                        "content": {
                            "application/json": {
                                "schema": {
                                    "$ref": "#/components/schemas/runsResponseSchema"
                                }
                            }
                        }
                    }
                }
            }
        },
        "/acts/hipersoft~pubmed-scraper/run-sync": {
            "post": {
                "operationId": "run-sync-hipersoft-pubmed-scraper",
                "x-openai-isConsequential": false,
                "summary": "Executes an Actor, waits for completion, and returns the OUTPUT from Key-value store in response.",
                "tags": [
                    "Run Actor"
                ],
                "requestBody": {
                    "required": true,
                    "content": {
                        "application/json": {
                            "schema": {
                                "$ref": "#/components/schemas/inputSchema"
                            }
                        }
                    }
                },
                "parameters": [
                    {
                        "name": "token",
                        "in": "query",
                        "required": true,
                        "schema": {
                            "type": "string"
                        },
                        "description": "Enter your Apify token here"
                    }
                ],
                "responses": {
                    "200": {
                        "description": "OK"
                    }
                }
            }
        }
    },
    "components": {
        "schemas": {
            "inputSchema": {
                "type": "object",
                "required": [
                    "query"
                ],
                "properties": {
                    "query": {
                        "title": "PubMed query",
                        "type": "string",
                        "description": "Any PubMed search query. Supports full syntax: terms, fields ([Title], [Author], [MeSH]), booleans, and date ranges. e.g. \"crispr gene editing\", \"asthma[MeSH] AND treatment\", \"covid-19 AND vaccine[Title]\"."
                    },
                    "dateFrom": {
                        "title": "Published from",
                        "type": "string",
                        "description": "Earliest publication date (YYYY/MM/DD or YYYY). Optional."
                    },
                    "dateTo": {
                        "title": "Published to",
                        "type": "string",
                        "description": "Latest publication date (YYYY/MM/DD or YYYY). Optional."
                    },
                    "includeAbstract": {
                        "title": "Include abstracts",
                        "type": "boolean",
                        "description": "Include the full abstract text for each article.",
                        "default": true
                    },
                    "maxResults": {
                        "title": "Max results",
                        "minimum": 1,
                        "maximum": 100000,
                        "type": "integer",
                        "description": "Maximum number of articles to return (a broad query can match tens of thousands).",
                        "default": 1000
                    },
                    "apiKey": {
                        "title": "NCBI API key (optional)",
                        "type": "string",
                        "description": "Optional NCBI API key to raise the request rate (3→10/sec) for faster large runs. Not required."
                    }
                }
            },
            "runsResponseSchema": {
                "type": "object",
                "properties": {
                    "data": {
                        "type": "object",
                        "properties": {
                            "id": {
                                "type": "string"
                            },
                            "actId": {
                                "type": "string"
                            },
                            "userId": {
                                "type": "string"
                            },
                            "startedAt": {
                                "type": "string",
                                "format": "date-time",
                                "example": "2025-01-08T00:00:00.000Z"
                            },
                            "finishedAt": {
                                "type": "string",
                                "format": "date-time",
                                "example": "2025-01-08T00:00:00.000Z"
                            },
                            "status": {
                                "type": "string",
                                "example": "READY"
                            },
                            "meta": {
                                "type": "object",
                                "properties": {
                                    "origin": {
                                        "type": "string",
                                        "example": "API"
                                    },
                                    "userAgent": {
                                        "type": "string"
                                    }
                                }
                            },
                            "stats": {
                                "type": "object",
                                "properties": {
                                    "inputBodyLen": {
                                        "type": "integer",
                                        "example": 2000
                                    },
                                    "rebootCount": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "restartCount": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "resurrectCount": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "computeUnits": {
                                        "type": "integer",
                                        "example": 0
                                    }
                                }
                            },
                            "options": {
                                "type": "object",
                                "properties": {
                                    "build": {
                                        "type": "string",
                                        "example": "latest"
                                    },
                                    "timeoutSecs": {
                                        "type": "integer",
                                        "example": 300
                                    },
                                    "memoryMbytes": {
                                        "type": "integer",
                                        "example": 1024
                                    },
                                    "diskMbytes": {
                                        "type": "integer",
                                        "example": 2048
                                    }
                                }
                            },
                            "buildId": {
                                "type": "string"
                            },
                            "defaultKeyValueStoreId": {
                                "type": "string"
                            },
                            "defaultDatasetId": {
                                "type": "string"
                            },
                            "defaultRequestQueueId": {
                                "type": "string"
                            },
                            "buildNumber": {
                                "type": "string",
                                "example": "1.0.0"
                            },
                            "containerUrl": {
                                "type": "string"
                            },
                            "usage": {
                                "type": "object",
                                "properties": {
                                    "ACTOR_COMPUTE_UNITS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATASET_READS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATASET_WRITES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "KEY_VALUE_STORE_READS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "KEY_VALUE_STORE_WRITES": {
                                        "type": "integer",
                                        "example": 1
                                    },
                                    "KEY_VALUE_STORE_LISTS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "REQUEST_QUEUE_READS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "REQUEST_QUEUE_WRITES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATA_TRANSFER_INTERNAL_GBYTES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATA_TRANSFER_EXTERNAL_GBYTES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "PROXY_RESIDENTIAL_TRANSFER_GBYTES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "PROXY_SERPS": {
                                        "type": "integer",
                                        "example": 0
                                    }
                                }
                            },
                            "usageTotalUsd": {
                                "type": "number",
                                "example": 0.00005
                            },
                            "usageUsd": {
                                "type": "object",
                                "properties": {
                                    "ACTOR_COMPUTE_UNITS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATASET_READS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATASET_WRITES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "KEY_VALUE_STORE_READS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "KEY_VALUE_STORE_WRITES": {
                                        "type": "number",
                                        "example": 0.00005
                                    },
                                    "KEY_VALUE_STORE_LISTS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "REQUEST_QUEUE_READS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "REQUEST_QUEUE_WRITES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATA_TRANSFER_INTERNAL_GBYTES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATA_TRANSFER_EXTERNAL_GBYTES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "PROXY_RESIDENTIAL_TRANSFER_GBYTES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "PROXY_SERPS": {
                                        "type": "integer",
                                        "example": 0
                                    }
                                }
                            }
                        }
                    }
                }
            }
        }
    }
}
```