# Europe PMC Scraper — Life-Science Papers & Full Text (`hipersoft/europepmc-scraper`) Actor Bulk-scrape life-science and biomedical literature from Europe PMC (40M+ records: PubMed, PMC, preprints, patents): title, abstract, authors, journal, year, DOI, PMID/PMCID, citation count, MeSH terms, open-access flag and full-text/PDF links. Thousands per run. No login, no API key. - **URL**: https://apify.com/hipersoft/europepmc-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 ## Europe PMC Scraper — Life-Science Papers & Full Text Bulk-scrape biomedical and life-science literature from **Europe PMC** — a 40M+ record index spanning **PubMed, PubMed Central, preprints, patents and agricultural literature**. Get titles, abstracts, authors, journals, years, DOIs, PMIDs/PMCIDs, **citation counts**, MeSH terms, open-access flags and **direct full-text / PDF links**. Thousands of records per run. No account, no API key. ### Features - 🔎 **Broad life-science coverage** — PubMed + PMC + preprints + patents in one search - 📄 **Full-text & PDF links** — direct links where the article is openly available - 📈 **Citation counts** — `citedByCount` per article - 🏷️ **Rich metadata** — MeSH terms, keywords, publication types, journal, IDs (DOI/PMID/PMCID) - 🔓 **Open-access filter** — restrict to freely readable articles - 📊 **Bulk & cursor-paginated** — scales to hundreds of thousands of records per query ### What you get One record per article: ```json { "id": "38512345", "source": "MED", "pmid": "38512345", "pmcId": "PMC10987654", "doi": "10.1038/s41586-024-00000-0", "title": "…", "authors": ["Jane A Smith", "…"], "journal": "Nature", "pubYear": 2024, "citedByCount": 37, "isOpenAccess": true, "hasPdf": true, "pdfUrl": "https://europepmc.org/articles/PMC10987654?pdf=render", "fullTextUrl": "https://europepmc.org/articles/PMC10987654", "meshTerms": ["…"], "url": "https://europepmc.org/article/MED/38512345", "abstract": "…" } ```` ### Input ```json { "query": "crispr AND cancer", "openAccessOnly": false, "maxResults": 5000 } ``` | Field | Description | |-------|-------------| | `query` | Europe PMC query (supports fields like `AUTH:`, `JOURNAL:`, `PUB_YEAR:`, booleans). | | `openAccessOnly` | Only open-access articles. | | `includeAbstract` | Include abstract text. | | `maxResults` | Max articles to return. | ### Use cases - **Systematic & literature reviews** — every relevant paper with abstracts and citations - **Full-text mining** — grab open-access PDF/HTML links at scale - **Bibliometrics** — rank by citations across PubMed + PMC + preprints - **Biomedical datasets** — build corpora with MeSH-indexed metadata ### 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 uses the public [Europe PMC](https://europepmc.org) REST API — no account, login or API key required. **How many articles can I scrape per run?** Set `maxResults` as high as you need — the API is cursor-paginated and scales to hundreds of thousands of records per query. **Is scraping Europe PMC legal?** Yes. Europe PMC openly publishes its life-science index through a public REST API, and this Actor reads only those openly available records and returns them as-is. **What format is the output?** Structured JSON — one record per article — exportable as JSON, CSV or Excel. Each record includes title, abstract, authors, journal, year, DOI, PMID/PMCID, citation count, MeSH terms, open-access flags and direct full-text/PDF links. **Can I filter by open access or use field search?** Yes. Flip `openAccessOnly` to keep only freely readable articles, and the `query` field supports Europe PMC syntax like `AUTH:`, `JOURNAL:`, `PUB_YEAR:` and booleans. ### Related Actors Building a biomedical literature dataset? These other hipersoft scrapers pair well with this one: - [PubMed Scraper](https://apify.com/hipersoft/pubmed-scraper) — biomedical papers, abstracts and MeSH terms from the NLM index - [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 public Europe PMC REST API. Returns its openly-available metadata as-is. This is an independent tool and is not affiliated with or endorsed by Europe PMC or EMBL-EBI. # Actor input Schema ## `query` (type: `string`): Europe PMC search query. Supports fields and booleans, e.g. "malaria AND vaccine", "AUTH:"Doudna"", "cancer AND PUB\_YEAR:2023". ## `openAccessOnly` (type: `boolean`): Return only open-access articles (full text freely available). ## `includeAbstract` (type: `boolean`): Include the abstract text for each article. ## `maxResults` (type: `integer`): Maximum articles to return (a broad query matches hundreds of thousands). ## Actor input object example ```json { "query": "crispr AND cancer", "openAccessOnly": false, "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 '' with your token const client = new ApifyClient({ token: '', }); // Prepare Actor input const input = { "query": "crispr AND cancer" }; // Run the Actor and wait for it to finish const run = await client.actor("hipersoft/europepmc-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 = { "query": "crispr AND cancer" } # Run the Actor and wait for it to finish run = client.actor("hipersoft/europepmc-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 AND cancer" }' | apify call hipersoft/europepmc-scraper --silent --output-dataset ``` ## MCP server setup ```json { "mcpServers": { "apify": { "command": "npx", "args": [ "mcp-remote", "https://mcp.apify.com/?tools=hipersoft/europepmc-scraper", "--header", "Authorization: Bearer " ] } } } ``` ## OpenAPI specification ```json { "openapi": "3.0.1", "info": { "title": "Europe PMC Scraper — Life-Science Papers & Full Text", "description": "Bulk-scrape life-science and biomedical literature from Europe PMC (40M+ records: PubMed, PMC, preprints, patents): title, abstract, authors, journal, year, DOI, PMID/PMCID, citation count, MeSH terms, open-access flag and full-text/PDF links. Thousands per run. No login, no API key.", "version": "1.0", "x-build-id": "hJF64WNdepVPNoack" }, "servers": [ { "url": "https://api.apify.com/v2" } ], "paths": { "/acts/hipersoft~europepmc-scraper/run-sync-get-dataset-items": { "post": { "operationId": "run-sync-get-dataset-items-hipersoft-europepmc-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": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK" } } } }, "/acts/hipersoft~europepmc-scraper/runs": { "post": { "operationId": "runs-sync-hipersoft-europepmc-scraper", "x-openai-isConsequential": false, "summary": "Executes an Actor and returns information about the initiated run in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$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": { "$ref": "#/components/schemas/runsResponseSchema" } } } } } } }, "/acts/hipersoft~europepmc-scraper/run-sync": { "post": { "operationId": "run-sync-hipersoft-europepmc-scraper", "x-openai-isConsequential": false, "summary": "Executes an Actor, waits for completion, and returns the OUTPUT from Key-value store in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$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": "Query", "type": "string", "description": "Europe PMC search query. Supports fields and booleans, e.g. \"malaria AND vaccine\", \"AUTH:\\\"Doudna\\\"\", \"cancer AND PUB_YEAR:2023\"." }, "openAccessOnly": { "title": "Open-access only", "type": "boolean", "description": "Return only open-access articles (full text freely available).", "default": false }, "includeAbstract": { "title": "Include abstracts", "type": "boolean", "description": "Include the abstract text for each article.", "default": true }, "maxResults": { "title": "Max results", "minimum": 1, "maximum": 100000, "type": "integer", "description": "Maximum articles to return (a broad query matches hundreds of thousands).", "default": 1000 } } }, "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 } } } } } } } } } } ```