Europe PMC Has a Free API — Search 40M+ Biomedical Papers With Full Text

#python #api #research #tutorial

PubMed is great, but it only gives you abstracts. What if you need the full text?

Europe PMC has 40M+ biomedical papers and 8M+ full-text articles available through a free API. No key required.

What Is Europe PMC?

Europe PMC is the European mirror of PubMed Central, but better:

40M+ articles (more than PubMed's 36M)
8M+ full-text papers (not just abstracts)
Preprints from bioRxiv and medRxiv included
No API key needed
No rate limits for reasonable use

Quick Start

import requests

# Search for papers
response = requests.get("https://www.ebi.ac.uk/europepmc/webservices/rest/search", params={
    "query": "CRISPR gene therapy clinical trials",
    "resultType": "core",
    "pageSize": 5,
    "format": "json"
})

for paper in response.json()["resultList"]["result"]:
    print(f"[{paper.get('pubYear', 'N/A')}] {paper['title']}")
    print(f"  Journal: {paper.get('journalTitle', 'N/A')}")
    print(f"  Cited by: {paper.get('citedByCount', 0)}")
    print(f"  Full text: {'Yes' if paper.get('isOpenAccess') == 'Y' else 'No'}")
    print()

Get Full Text of a Paper

# Get full text XML for a PMC article
pmcid = "PMC7610813"  # Example
resp = requests.get(f"https://www.ebi.ac.uk/europepmc/webservices/rest/{pmcid}/fullTextXML")
if resp.status_code == 200:
    print(f"Full text length: {len(resp.text):,} characters")
    # Parse with xml.etree or BeautifulSoup

Search by Author or Affiliation

# Papers by a specific author
response = requests.get("https://www.ebi.ac.uk/europepmc/webservices/rest/search", params={
    "query": 'AUTH:"Jennifer Doudna" AND CRISPR',
    "resultType": "core",
    "pageSize": 5,
    "format": "json"
})

for p in response.json()["resultList"]["result"]:
    print(f"[{p.get('pubYear')}] {p['title'][:70]}")
    print(f"  Cited: {p.get('citedByCount', 0):,}")

Citation Network

# Get papers that cite a specific paper
pmid = "26544986"  # Example PMID
resp = requests.get(f"https://www.ebi.ac.uk/europepmc/webservices/rest/MED/{pmid}/citations", params={
    "page": 1,
    "pageSize": 5,
    "format": "json"
})

data = resp.json()
print(f"Total citations: {data.get('hitCount', 0)}")
for c in data.get("citationList", {}).get("citation", []):
    print(f"  [{c.get('pubYear')}] {c.get('title', 'N/A')[:60]}")