Europe PMC API

Europe PMC is a single search surface over PubMed abstracts, PMC full text, preprints (bioRxiv, medRxiv, Research Square, SSRN and others), patents, NHS guidelines, and theses. It is the one API in this skill that does keyword search across those corpora at once.

Reach for it when you need something the others cannot do:

• Keyword search of bioRxiv/medRxiv preprints. The preprint servers' own APIs have no keyword search at all (see references/biorxiv.md). Europe PMC indexes them and filters with SRC:"PPR".
• Search inside full text, not just titles and abstracts, with the results-limiting filters (HAS_FT:Y, OPEN_ACCESS:Y) applied server-side.
• Full text that fails honestly. fullTextXML returns a clean 404 when an article is not open access, where NCBI eFetch returns HTTP 200 with metadata and no <body> (see the hazard section of references/pmc.md).

All figures below verified 2026-07-27.

Base URL

https://www.ebi.ac.uk/europepmc/webservices/rest

Authentication

None. No key, no email parameter, no registration.

Rate Limits

No published per-second limit. Europe PMC asks for reasonable use and recommends cursorMark pagination over deep page offsets for large walks. Keep concurrency low and serialize long walks.

Key Endpoints

1. Search

GET /search?query={query}&format=json&pageSize={n}&resultType={type}

Example -- preprints about CRISPR:

curl -s --get "https://www.ebi.ac.uk/europepmc/webservices/rest/search" \
  --data-urlencode 'query=CRISPR AND SRC:"PPR"' \
  --data-urlencode 'format=json' \
  --data-urlencode 'pageSize=2' \
  --data-urlencode 'resultType=lite'

Returns hitCount 13341 with resultList.result[] entries whose id values look like PPR1283561 and source is PPR.

Response envelope:

{
  "version": "6.9",
  "hitCount": 13341,
  "nextCursorMark": "AoIIQExCVyg1NTg2NjE3NQ==",
  "nextPageUrl": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?...",
  "request": {"queryString": "CRISPR AND SRC:\"PPR\"", "resultType": "lite", "cursorMark": "*", "pageSize": 2},
  "resultList": {"result": [...]}
}

The echoed request.queryString is the query as parsed -- diff it against what you sent to catch a mangled or truncated query before trusting hitCount.

**Errors arrive with HTTP 200 and no resultList.** pageSize=1001 returns:

{"errCode": 404, "errMsg": "Invalid page size provided. Valid size is between 1 and 1000"}

Note the errCode is 404 inside a 200 response. Check for errCode / the absence of resultList before indexing into results -- neither the HTTP status nor an exception will tell you.

2. Full text XML

GET /{PMCID}/fullTextXML

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7029759/fullTextXML

Returns a JATS <article> (not wrapped in <pmc-articleset> the way eFetch is). Pipe it through scripts/jats_to_text.py, which handles both wrappers.

404 means this endpoint did not supply the requested XML. Check the PMCID and metadata before attributing it to licensing; an absent/wrong identifier can also fail. The historical PMC1500000 probe returned 404, but a single failure is not a universal OA classifier.

3. Citations and references

GET /{source}/{id}/citations?format=json&pageSize={n}&page={n}
GET /{source}/{id}/references?format=json&pageSize={n}&page={n}

source is the corpus code: MED (PubMed), PMC, PPR (preprints), PAT (patents), AGR, CBA, CTX, ETH, HIR, NBK.

https://www.ebi.ac.uk/europepmc/webservices/rest/MED/32117569/citations?format=json&pageSize=1

Returns hitCount plus citationList.citation[] (or referenceList.reference[]). Both wrap the list in a corpus-specific key, so parse by endpoint rather than assuming resultList.

4. Supplementary files and annotations

GET /{PMCID}/supplementaryFiles

This route takes a PMCID without a source segment, e.g. /PMC5998401/supplementaryFiles, and returns a ZIP archive, not JSON. /MED/32117569/supplementaryFiles is not the documented route. Its 404 cannot establish that an article has no supplements. Inspect hasSuppl in resultType=core and the archive content; non-OA images may be excluded.

The previously listed /textMinedTerms/{semanticType} route is not in the current Articles REST operation list and was not verified as supported. Use PubTator3 for this skill's entity workflow, or consult the official Europe PMC Annotations API. Do not interpret a legacy-route 404 as evidence that no annotations exist.

Query Language

Field-prefixed terms combined with AND / OR / NOT (uppercase), quoted phrases, and parentheses.

A bare term with no prefix searches title, abstract, and full text together.

The pattern that closes the preprint gap:

curl -s --get "https://www.ebi.ac.uk/europepmc/webservices/rest/search" \
  --data-urlencode 'query=(SRC:"PPR" AND PUBLISHER:"bioRxiv" AND "organoid")' \
  --data-urlencode 'format=json' \
  --data-urlencode 'pageSize=2' \
  --data-urlencode 'resultType=lite'

hitCount 1972, with bookOrReportDetails.publisher confirming bioRxiv on each hit. Take the doi (a 10.1101/... preprint DOI) from these results and hand it to the bioRxiv API for preprint-specific metadata such as the published-version link.

Result Object (resultType=core, key fields)

{
  "id": "37917583",
  "source": "MED",
  "pmid": "37917583",
  "pmcid": "PMC10680139",
  "doi": "10.1016/j.celrep.2023.113339",
  "title": "...",
  "authorString": "Smith J, Jones A.",
  "journalInfo": {"volume": "42", "journal": {"title": "Cell reports"}},
  "pubYear": "2023",
  "abstractText": "...",
  "isOpenAccess": "Y",
  "inEPMC": "Y",
  "hasPDF": "Y",
  "hasSuppl": "Y",
  "citedByCount": 14,
  "fullTextUrlList": {"fullTextUrl": [{"documentStyle": "pdf", "url": "..."}]}
}

**The boolean-ish fields are the strings "Y" / "N", not JSON booleans.** A truthiness test passes for "N", so compare explicitly. pmcid is absent -- not null -- when the article is not in PMC.

Preprint (SRC:"PPR") records differ in shape: the server name lives in bookOrReportDetails.publisher, and journalInfo is absent. Do not assume one schema across corpora.

Identifiers

Every result carries id + source, and that pair is the key -- id alone is not unique across corpora. Endpoints that take an article path want {source}/{id}, e.g. MED/32117569. Preprint IDs are PPR-prefixed (PPR1283561) and are Europe PMC's own, not bioRxiv's; use the record's doi to cross-reference.

Pagination and Count Reconciliation

1. hitCount on the first response is the total.
2. Request with cursorMark=*, then pass the returned nextCursorMark on each subsequent call.
3. **Stop when resultList.result is empty or nextCursorMark is absent, null, or equals the cursor you sent.** A historical walk echoed the cursor on an empty final page; a one-hit public query on 2026-09-30 omitted it. Do not assume either termination shape is universal.
4. Reconcile retrieved count against hitCount and report both.

Historical verified walk (AUTH:"Doudna J" AND PUB_YEAR:2013 AND SRC:"MED", pageSize=5): pages of 5, 5, 5, 4, then a 5th request returning 0 results with the cursor unchanged. Retrieved 19, hitCount 19.

scripts/paginate.py --api europepmc implements this, including the repeated-cursor stop condition.

Deep page offsets degrade and are capped; cursorMark is the supported path for anything past a few pages.

Official sources reviewed 2026-09-30

• https://europepmc.org/RestfulWebService