A PubMed citation carries identifiers, journal details, MeSH terms and its authors. Our PubMed scraper delivers them as rows, with authors disambiguated and trial identifiers resolved.
Plans from €169/month · Free project assessment · Reply within 1 business day
ScrapeIt builds and runs the pipeline as a managed service. You define the corpus by subject terms, journals, authors, institutions or date range; we collect the records, resolve authors and affiliations, keep the subject indexing structured, and hand back CSV, JSON, Excel or a push into your warehouse.
Pacing and proxy rotation are part of the service. That is why access here stays stable, and it is why we can quote a schedule we will actually keep. The same data is also available through the ScrapeIt PubMed API, an endpoint we host, with access by key.
Citation metadata is public. Abstracts come with the record, full text is included where the article is open access, and open access status is recorded on every row rather than leaving you to find out later. We collect only publicly available data - everything a visitor can see on PubMed - and we collect it legally.
The citation record covers PubMed identifier, DOI where present, article title, abstract, journal title and abbreviation, ISSN, volume, issue, pagination, publication date and the electronic publication date where they differ, publication type, and language.
Authors come as rows rather than a string. Each carries surname, given name, initials, position in the author list, corresponding author flag where marked, and the affiliation as published. Author position matters: first and last author carry very different meaning in biomedical publishing, and a flattened author field throws that away.
Subject indexing is delivered structured. MeSH descriptors and qualifiers are kept as separate terms with their major topic flags intact, which is what makes precise selection possible. Filtering a corpus by a controlled vocabulary term is a categorically better operation than matching words in a title, and this source is one of the few where that vocabulary exists.
Identifiers that connect outward are extracted deliberately: trial registration numbers, grant and funding identifiers, and full text links including PubMed Central identifiers where the article is open. Those are the fields that let a literature dataset join to a trial registry, to a funder database or to the text itself.
Affiliations are normalised to institutions with the raw string preserved, and every row carries the retrieval timestamp.
Trial registration numbers appear in a good many clinical papers and are the bridge to a registry dataset. Extracted properly, they let you ask what a trial actually reported rather than only what it planned, and they are the reason clients usually buy this alongside clinical trial collection.
Grant and funding identifiers support a different question: what a funder produced, and where. They need the same institutional normalisation as affiliations before they aggregate sensibly.
Full text availability is recorded rather than assumed. Where an article is open access with a PubMed Central identifier, that is captured and the text can be included. Where it is not, we record the link and stop, because we never go behind publisher paywalls.
Records change after publication. Indexing is added, corrections and retractions are issued, and a retraction that your dataset never noticed is a genuine hazard in medical analysis. We re-check records on a schedule and deliver update and retraction status as fields, so a corpus stays honest instead of quietly ageing.
PubMed is the National Library of Medicine index of biomedical literature: citations and abstracts across tens of millions of records, with subject indexing, author affiliations and links out to full text where it exists.
Each record shows a visitor the article title, the author list with affiliations, the journal and publication date, the abstract, the publication type, MeSH subject terms, and the identifiers that connect outward: DOI, PubMed Central link, trial registration and grant numbers. All of it can be collected.
Getting to the records is handled on our side, with requests paced and proxies rotated, so collection stays stable from a narrow topic to a whole field.
The work, therefore, is not access. It is everything after retrieval: resolving authors who share names, normalising institutional affiliations that are written forty different ways, keeping the subject indexing usable, and joining records to trials, grants and full text. That is where a literature pipeline succeeds or fails.
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Delivery: CSV, JSON or XLSX files, our API or a JSON feed. MCP server on request.
Full plan details →Retrieving PubMed records is only the first step. The reason literature projects stall is that the records do not join to each other cleanly, and the two fields that break are the ones everybody assumes are simple.
Author names collide constantly. Common surnames with a single initial can cover hundreds of distinct researchers, and the same researcher appears with and without a middle initial, with a maiden name, and with the given name spelled two ways. Counting publications per researcher without disambiguation produces numbers that are confidently wrong. We disambiguate using co-authorship networks, affiliation history, subject overlap and identifiers where the article carries them, and we mark confidence rather than pretending it is certain.
Affiliations are worse, because they are free text. One university appears as its English name, its local name, an abbreviation, a department first, a hospital that belongs to it, and several misspellings. Institutional analysis is impossible until those collapse to one entity, and doing it after the data has landed is far harder than doing it during the pipeline.
The third problem is the corpus definition itself. A keyword search returns a pile with unclear edges. Selection through the controlled vocabulary, with the qualifiers and major topic flags intact, gives a corpus somebody else can reproduce, which is what any serious analysis requires.
The fourth is joining outward. A literature record is most useful when it is attached to a trial, a grant or a full text. Those identifiers are present in the source and routinely dropped by naive pipelines.
Learn how to use web scraping to solve data problems for your organization
Leveraging advances in technology, the AI-powered web scraper has skyrocketed in demand and is helping to expand capabilities by automating tedious daily tasks and speeding up data collection from thousands of websites several times over.
Web scraping is a method of obtaining web data by extracting it from pages of web resources with the help of a program, that is, in automatic mode. It is used to syntactically convert web pages into more usable forms.
If you specialize in machine learning, you need to feed large amounts of data to the algorithms. Web scraping is the easiest and the most efficient method of collecting the data from all over the Internet.
ScrapeIt is a managed extraction company, not a tool you have to learn. Our team builds the pipeline, watches it as pages and record formats change, and repairs it before your analysis goes stale.
You see a sample first, in your format, over your corpus definition, with authors disambiguated and affiliations normalised so you can judge the hard part on real records.
Yes. We collect only publicly available data - citations, abstracts, authors and affiliations, MeSH terms, trial and grant identifiers, everything a visitor can see on PubMed - and we collect it legally. Requests are paced as part of the service, which is why access here stays stable.
With disambiguation rather than hope. We use co-authorship networks, affiliation history, subject overlap and any author identifiers the article carries, then mark each assignment with a confidence level. Publication counts per researcher built without this step are confidently wrong, and common surnames with a single initial can cover hundreds of distinct people.
Yes, and it is usually the most valuable part of the job. Affiliations are free text: one university appears under its English name, its local name, several abbreviations, a department, an affiliated hospital and a few misspellings. We collapse them to one institution, keep the raw string on the row, and deliver both so any aggregate can be audited.
Abstracts where they are published in the record, and full text where the article is open access with a PubMed Central identifier. Open access status is recorded on every row rather than left for you to discover downstream. We never go behind publisher paywalls.
By re-checking records on a schedule and delivering update and retraction status as fields. A retracted paper sitting unmarked in a medical corpus is a real hazard, and indexing is also added after initial publication, so a set retrieved once and never refreshed quietly ages into something misleading.
Step 1 - Make a Request
You share your needs, expectations, and desired timeframe. We’ll suggest the best solution based on your request and budget.
Step 2 - Configuring Custom Web Crawlers
Our specialists configure the crawlers and extract a sample dataset for your review before proceeding with the full-scale extraction.
Step 3 - Collect and Deliver
Once you approve the sample, we launch the project and start full data collection. We gather, filter, and structure the data for easy use, delivering it on time in your preferred format.
Step 4 - Maintain and Support
Our team manages ongoing processes, monitors website changes, and supports all data extraction cycles. We can also help integrate data into your systems or create dashboards to simplify analysis.
PubMed data from €169/month. Free project assessment, reply within 1 business day.
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