europe-pmc-api

Europe PMC API Guide

Overview

Europe PMC (PubMed Central) is a free, comprehensive biomedical literature database maintained by the European Bioinformatics Institute (EMBL-EBI) as part of a network of 32 European funders. It provides access to over 40 million biomedical and life sciences publications, including abstracts from PubMed/MEDLINE, full-text articles from PubMed Central, patents from the European Patent Office, and preprints from biomedical preprint servers.

Europe PMC extends beyond PubMed by integrating additional European content, preprints, and rich text-mined annotations. It provides links to biological databases (UniProt, Protein Data Bank, etc.), grant information from funders, and citation data. The annotation features include gene/protein mentions, disease names, organism identifiers, and chemical entities extracted via machine learning.

The API is free, requires no authentication, and supports 10 requests per second. It returns JSON or XML and offers advanced query syntax with field-specific searches, boolean operators, and date range filters.

Authentication

No authentication required. The Europe PMC API is fully open. No API key, registration, or email is needed. The API enforces a rate limit of 10 requests per second per IP address. Including a descriptive User-Agent header is considered good practice.

Core Endpoints

Search: Full-Text Literature Search

• URL: GET https://www.ebi.ac.uk/europepmc/webservices/rest/search
• Parameters:

  Param	Type	Required	Description
  query	string	Yes	Search query (supports field codes: TITLE, AUTH, JOURNAL, DOI, etc.)
  format	string	No	Response format: json (default) or xml
  resultType	string	No	lite (default) or core (includes full abstract and metadata)
  pageSize	integer	No	Results per page (default: 25, max: 1000)
  cursorMark	string	No	Cursor for deep pagination (use nextCursorMark from response)
  sort	string	No	Sort field: RELEVANCE, CITED, DATE (default: RELEVANCE)
  synonym	boolean	No	Enable MeSH synonym expansion (default: true)

• Example:

  curl "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=CRISPR+AND+cancer&format=json&resultType=core&pageSize=10&sort=CITED+desc"
  

• Response: JSON with hitCount, nextCursorMark, and resultList.result array. Each result contains id, source (MED, PMC, PPR, PAT), pmid, pmcid, doi, title, authorString, journalTitle, pubYear, abstractText, citedByCount, isOpenAccess, and fullTextUrlList.

Citations: Papers Citing a Publication

• URL: GET https://www.ebi.ac.uk/europepmc/webservices/rest/{source}/{id}/citations
• Parameters:

  Param	Type	Required	Description
  source	string	Yes	Source database: MED (PubMed), PMC, PPR (preprint), PAT (patent)
  id	string	Yes	The publication ID (PMID, PMCID, etc.)
  format	string	No	json or xml
  page	integer	No	Page number (default: 1)
  pageSize	integer	No	Results per page (default: 25)

• Example:

  curl "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33116299/citations?format=json&pageSize=10"
  

• Response: JSON with hitCount and citationList.citation array containing citing publication metadata.

References: Papers Cited by a Publication

• URL: GET https://www.ebi.ac.uk/europepmc/webservices/rest/{source}/{id}/references
• Parameters:

  Param	Type	Required	Description
  source	string	Yes	Source database
  id	string	Yes	The publication ID
  format	string	No	json or xml
  page	integer	No	Page number
  pageSize	integer	No	Results per page

• Example:

  curl "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33116299/references?format=json&pageSize=50"
  

• Response: JSON with referenceList.reference array containing reference metadata.

Rate Limits

The API enforces a rate limit of 10 requests per second per IP address. There is no daily request cap. Exceeding the rate limit returns HTTP 429. For bulk data access, Europe PMC provides OAI-PMH harvesting, FTP bulk downloads, and SPARQL endpoint access. Cursor-based pagination (using cursorMark) is required for retrieving beyond the first 10,000 results.

Common Patterns

Systematic Review Search

Perform a structured biomedical search with MeSH terms and date filters:

curl -s "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=(TITLE:immunotherapy+AND+TITLE:melanoma)+AND+(PUB_YEAR:[2022+TO+2026])&format=json&resultType=core&pageSize=25&sort=CITED+desc" | jq '.resultList.result[] | {title: .title, journal: .journalTitle, year: .pubYear, citations: .citedByCount, oa: .isOpenAccess}'

Find Preprints Related to a Topic

Search specifically in the preprint sources indexed by Europe PMC:

curl -s "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=(SRC:PPR)+AND+large+language+models+AND+biology&format=json&pageSize=10" | jq '.resultList.result[] | {title: .title, source: .source, year: .pubYear, doi: .doi}'

Build a Citation Map for a Key Paper

Retrieve both citations and references to map a paper's scholarly context:

# Get papers that cite the target
curl -s "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33116299/citations?format=json&pageSize=50" | jq '.citationList.citation | length'

# Get papers referenced by the target
curl -s "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33116299/references?format=json&pageSize=100" | jq '.referenceList.reference | length'

References

• Official documentation: https://europepmc.org/RestfulWebService
• Europe PMC search syntax: https://europepmc.org/searchsyntax
• Europe PMC annotations API: https://europepmc.org/AnnotationsApi