| name | europepmc-search |
| description | Search Europe PMC for life-science literature and retrieve abstracts, citations, and open-access full text (XML/plain text) by PMCID. Use when the user wants broad biomedical literature discovery or open-access full text. Public API, no credential needed. |
| license | Apache-2.0 |
Europe PMC Search (Codex-native)
Codex-native adaptation of Google DeepMind's literature-search-europepmc skill
(science-skills, Apache-2.0).
Uses the public Europe PMC REST API directly.
Gates (ask before proceeding)
- Terms notice: on first use, tell the user to review the Europe PMC terms
(https://europepmc.org/) and to check each retrieved paper's own license;
record the notice in provenance.
- Network / install: read-only public HTTP; keep to ~1 request/second. If you
write helper code, run it via
uv run, never bare python3.
Workflow
Search first with science_search_europepmc; use the direct API for cursor
pagination, citations, annotations, or open-access full text.
- Search:
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=<terms>&format=json&pageSize=<n>.
Europe PMC covers 40M+ abstracts across many sources (PubMed, PMC, preprints,
patents). Use its query syntax (fielded terms, AUTH:, PUB_YEAR:, etc.).
- For full text, restrict to open access (append
OPEN_ACCESS:y to the
query) and fetch by PMCID:
https://www.ebi.ac.uk/europepmc/webservices/rest/PMC<ID>/fullTextXML. Only
open-access articles have retrievable full text.
- Citations / references are available via the
.../MED/<PMID>/citations and .../references endpoints when needed.
- Write responses to a file and parse them; do not dump large XML to stdout.
- Report each kept article with title, id (PMID/PMCID/DOI), source, year,
one-line relevance, and URL. List the URLs of every paper used.
- Provenance & review: record queries and cited ids with
$science-provenance; check claims with $science-review.
Boundaries
- Cite only ids actually returned; never invent PMIDs/PMCIDs/DOIs or abstracts.
- Full text exists only for open-access items; respect each article's license
before reproducing content.
- Search results are references, not clinical advice.
