# PubMed Scraper - Biomedical Literature & Citations (`benthepythondev/pubmed-scraper`) Actor PubMed Scraper for the official NCBI PubMed API. Search 37M+ biomedical citations; extract title, authors, journal, publication date, DOI, PMID, article type and links. Supports PubMed field tags and sorting. For systematic reviews, medical research and bibliometrics. Keyless and fast. - **URL**: https://apify.com/benthepythondev/pubmed-scraper.md - **Developed by:** [ben](https://apify.com/benthepythondev) (community) - **Categories:** Automation, Developer tools - **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks - **User rating**: No ratings yet ## Pricing Pay per usage This Actor is paid per platform usage. The Actor is free to use, and you only pay for the Apify platform usage, which gets cheaper the higher subscription plan you have. Learn more: https://docs.apify.com/platform/actors/running/actors-in-store#pay-per-usage ## 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.md): ```bash npm install apify-client ``` In Python projects, use official [Python client library](https://docs.apify.com/api/client/python.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/platform/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 — Biomedical Literature & Citations **Search [PubMed](https://pubmed.ncbi.nlm.nih.gov) — the U.S. National Library of Medicine's database of 37M+ biomedical citations.** Built for **medical research, systematic reviews, life-sciences analytics, and clinical databases**. Keyless, fast and reliable — no proxy or browser needed. ### What you get Per article: - **title**, **pmid** - **authors**, **author_count**, **last_author** - **journal**, **journal_abbr**, **issn** - **pub_date**, **epub_date**, **volume**, **issue**, **pages** - **pub_type**, **language** - **doi**, **doi_url**, **pmc_id** - **url** (PubMed page) - **search_query**, **scraped_at** ### Why this Actor | | PubMed Scraper | Manual search | Raw E-utilities | |---|---|---|---| | Official NCBI data | Yes | Yes | Yes | | Clean flat output | Yes | — | XML/JSON glue | | Search field tags | Yes | Yes | DIY | | Pay per result | Yes | — | — | ### Input | Field | Type | Description | |---|---|---| | `searchQuery` | string | PubMed term (supports field tags like `[Title]`) | | `sortBy` | string | Relevance / Publication Date / Most Recent | | `maxResults` | integer | Max articles to return | #### Example input ```json { "searchQuery": "crispr cas9 AND cancer[Title]", "sortBy": "newest", "maxResults": 100 } ```` ### Sample output ```json { "pmid": "42206706", "title": "Non-Viral CRISPR carriers: transient gene delivery", "authors": ["Smith J", "Doe A"], "journal": "Drug Delivery", "pub_date": "2026 Dec 31", "doi": "10.1080/10717544.2026.2614125", "url": "https://pubmed.ncbi.nlm.nih.gov/42206706/" } ``` ### Use cases - **Systematic reviews** — collect citations for a research question - **Medical research** — monitor new publications on a topic - **Bibliometrics** — analyse journals, authors and trends - **Clinical databases** — enrich records with PubMed metadata ### Pricing Pay-per-result. You are charged only for the articles returned — empty runs cost nothing. ### Notes & legal - Uses the official NCBI PubMed E-utilities API. Respect NCBI's usage policy and rate limits (max 3 requests/second without an API key). - Use data only for lawful purposes. ### Related actors More scrapers from the same author: - [OpenAlex Scraper](https://apify.com/benthepythondev/openalex-scraper) — academic papers & citations - [arXiv Scraper](https://apify.com/benthepythondev/arxiv-scraper) — 2M+ scientific papers, abstracts & PDFs - [Reddit Archive Scraper](https://apify.com/benthepythondev/reddit-archive-scraper) — years of historical posts & comments # Actor input Schema ## `searchQuery` (type: `string`): PubMed search term. Supports field tags, e.g. 'crispr', 'cancer immunotherapy', 'covid-19 AND vaccine\[Title]'. ## `sortBy` (type: `string`): How to sort the results. ## `maxResults` (type: `integer`): Maximum number of articles to return. ## Actor input object example ```json { "searchQuery": "crispr", "sortBy": "relevance", "maxResults": 25 } ``` # 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 '' with your token const client = new ApifyClient({ token: '', }); // Prepare Actor input const input = { "searchQuery": "crispr", "maxResults": 25 }; // Run the Actor and wait for it to finish const run = await client.actor("benthepythondev/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 '' with your token. client = ApifyClient("") # Prepare the Actor input run_input = { "searchQuery": "crispr", "maxResults": 25, } # Run the Actor and wait for it to finish run = client.actor("benthepythondev/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 '{ "searchQuery": "crispr", "maxResults": 25 }' | apify call benthepythondev/pubmed-scraper --silent --output-dataset ``` ## MCP server setup ```json { "mcpServers": { "apify": { "command": "npx", "args": [ "mcp-remote", "https://mcp.apify.com/?tools=benthepythondev/pubmed-scraper", "--header", "Authorization: Bearer " ] } } } ``` ## OpenAPI specification ```json { "openapi": "3.0.1", "info": { "title": "PubMed Scraper - Biomedical Literature & Citations", "description": "PubMed Scraper for the official NCBI PubMed API. Search 37M+ biomedical citations; extract title, authors, journal, publication date, DOI, PMID, article type and links. Supports PubMed field tags and sorting. For systematic reviews, medical research and bibliometrics. Keyless and fast.", "version": "1.0", "x-build-id": "0JgLM1wk9WOAq2i11" }, "servers": [ { "url": "https://api.apify.com/v2" } ], "paths": { "/acts/benthepythondev~pubmed-scraper/run-sync-get-dataset-items": { "post": { "operationId": "run-sync-get-dataset-items-benthepythondev-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/benthepythondev~pubmed-scraper/runs": { "post": { "operationId": "runs-sync-benthepythondev-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/benthepythondev~pubmed-scraper/run-sync": { "post": { "operationId": "run-sync-benthepythondev-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": [ "searchQuery" ], "properties": { "searchQuery": { "title": "Search Query", "type": "string", "description": "PubMed search term. Supports field tags, e.g. 'crispr', 'cancer immunotherapy', 'covid-19 AND vaccine[Title]'." }, "sortBy": { "title": "Sort By", "enum": [ "relevance", "newest", "most_recent" ], "type": "string", "description": "How to sort the results.", "default": "relevance" }, "maxResults": { "title": "Max Results", "minimum": 1, "maximum": 10000, "type": "integer", "description": "Maximum number of articles to return.", "default": 50 } } }, "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 } } } } } } } } } } ```