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SKILL.md
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)
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:
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'
