brycewang-stanford/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