PubMed Scraper — Biomedical Research, Abstracts & Citations

Search and extract biomedical research papers from PubMed — the world's largest database of life sciences and biomedical literature. Get full metadata, abstracts, MeSH terms, citations, author networks, and smart analytics. Powered by the official NCBI Entrez API.

What can this scraper do?

• Search by any query — use simple keywords or advanced PubMed syntax with MeSH terms and field tags
• Full metadata extraction — authors with affiliations and ORCID, journal info, DOI, publication types, grants, chemicals
• Abstracts — complete structured abstracts for every article
• MeSH terms — Medical Subject Headings with major topic indicators and qualifiers
• Citation data — cited-by counts and reference PMIDs
• Smart analytics — author networks, topic trends by year, top journals, funding agencies, geographic distribution
• Multiple databases — PubMed, PubMed Central (PMC), Gene, Protein
• No API key required — works out of the box, optional API key for faster rate limits

Why use PubMed Scraper?

Use case	How it helps
Literature review	Collect hundreds of papers on any topic with full abstracts and metadata
Competitive intelligence	Track research output from specific institutions or authors
Pharma & biotech research	Monitor clinical trials, drug targets, and therapeutic areas
Grant landscape analysis	Identify top funding agencies and grant patterns in your field
Bibliometric analysis	Analyze publication trends, co-authorship networks, and journal distributions
Academic research	Build structured datasets for systematic reviews and meta-analyses
Trend monitoring	Track emerging topics through MeSH term trends over time

Output data

Article data

Each article includes all available metadata:

Field	Description
PMID & PMCID	PubMed and PubMed Central identifiers
Title	Article title
Authors	Full list with last name, first name, affiliations, and ORCID
Abstract	Complete abstract text
Journal	Name, abbreviation, ISSN, volume, issue, pages
Publication date	ISO format date
DOI	Digital Object Identifier
Publication types	Journal Article, Review, Clinical Trial, Meta-Analysis, etc.
MeSH terms	Descriptors with qualifiers and major topic flags
Keywords	Author-provided keywords
Grant info	Grant IDs, agencies, and countries
Chemicals	Registry numbers and substance names
Full text URL	PMC link for open access articles
Cited-by count	Number of citing articles (when enabled)
References	First 10 reference PMIDs (when enabled)
Language & country	Publication language and journal country
Clinical trial ID	Associated trial registry number
Retraction status	Whether the article has been retracted
Conflict of interest	Author disclosures

Smart analytics

Every run can include an automatic analytics summary:

Analytics	What you get
Top authors	Most prolific authors with collaborator counts
Author networks	Co-authorship connections and top collaborators
Topic trends	MeSH major topics by year
Journal distribution	Top journals by article count
Funding agencies	Top grant sources
Geographic distribution	Articles by country
Publication types	Breakdown by article type
Open access rate	Percentage of open access articles
Publications by year	Yearly publication volume

Filters & options

Filter	Options
Date range	From/to dates (YYYY/MM/DD format)
Sort by	Relevance, Publication date, Most cited
Species	All, Human only, Animal only
Language	Filter by publication language (eng, fre, de, etc.)
Publication type	Journal Article, Review, Clinical Trial, Meta-Analysis, etc.
Database	PubMed, PMC, Gene, Protein
Include abstract	Full abstract text (on by default)
Include MeSH	Medical Subject Headings (on by default)
Include citations	Cited-by counts and references
Include full text links	PMC open access URLs
Include analytics	Smart analytics summary

How much does it cost?

PubMed Scraper uses a pay-per-result model at $0.03 per result. No monthly fees — you only pay for the data you collect.

Results	Cost
100 articles	$3.00
500 articles	$15.00
1,000 articles	$30.00
10,000 articles	$300.00

Platform costs are included in the per-result price.

Input examples

Basic search

{
  "queries": ["breast cancer immunotherapy"],
  "maxResults": 100,
  "includeAbstract": true,
  "includeMeshTerms": true,
  "includeAnalytics": true
}

Advanced PubMed syntax with date filter

{
  "queries": ["COVID-19[MeSH] AND vaccine[tiab]"],
  "maxResults": 200,
  "dateFrom": "2024/01/01",
  "dateTo": "2026/05/18",
  "sortBy": "pub_date",
  "species": "human",
  "language": ["eng"]
}

Multi-query research with citations

{
  "queries": ["CRISPR gene therapy", "base editing clinical trials"],
  "maxResults": 50,
  "includeCitations": true,
  "includeFullTextLinks": true,
  "includeAnalytics": true
}

Systematic review — specific publication types

{
  "queries": ["diabetes type 2 metformin"],
  "maxResults": 500,
  "pubTypes": ["Clinical Trial", "Randomized Controlled Trial"],
  "species": "human",
  "sortBy": "cited_by_count",
  "dateFrom": "2020/01/01"
}

PubMed Central full text search

{
  "queries": ["machine learning drug discovery"],
  "database": "pmc",
  "maxResults": 100,
  "includeFullTextLinks": true,
  "includeAnalytics": true
}

Tips for best results

1. Start small — test with 10-20 results to verify your query before scaling up
2. Use PubMed syntax — field tags like [MeSH], [tiab], [au] give precise control over search results
3. API key — get a free NCBI API key to increase rate limits from 3 to 10 requests/second
4. Citations wisely — enable includeCitations only when needed, it requires extra API calls
5. Species filter — use human for clinical research, animal for preclinical studies
6. Sort by citations — cited_by_count helps find the most impactful papers in your field
7. Combine queries — use multiple queries to cover different aspects of your research topic

Limitations

• PubMed API returns up to 9,999 results per query (NCBI hard cap). For larger datasets, split into narrower date windows
• Citation counts are approximate and may not reflect the latest data
• Full text is only available for open access articles in PMC
• Rate limits: 3 requests/second without API key, 10 requests/second with key
• Analytics summary is included as the last record in the dataset (field type: "analytics")