| name | literature-search-europepmc |
| description | > Search Europe PMC for scientific literature and download open-access full texts and PDFs. Retrieve full-text XML/plain text by PMCID, get citation lists and bibliography. |
Europe PMC Database
A skill for searching, downloading, and exploring open-access papers from
Europe PMC — a comprehensive, free life-science
literature database with over 43 million abstracts and 9 million full-text
articles.
Prerequisites
uv: Read the uv skill and follow its Setup instructions to ensure
uv is installed and on PATH.- User Notification: If LICENSE_NOTIFICATION.txt does not already exist in
this skill directory then (1) prominently notify the user to check the terms
at https://europepmc.org/ and to always check the license of the papers
retrieved by the skill for any restrictions, then (2) create the file
recording the notification text and timestamp.
Core Rules
- Open Access Only: This skill exclusively searches open-access content.
The script automatically appends
OPEN_ACCESS:y to every search query. Do
NOT remove or override this filter.
- NEVER run python3 or python3 -c directly: the system Python does not
necessarily have all key dependencies. Do not attempt to pip install or
create new venvs.
- Use the Wrapper: ALWAYS use the provided script rather than calling the
API directly. The script handles rate limiting (1 req/s) and errors.
- Output Files: All subcommands require
--output to write results to a
file. Read the output file separately to avoid context overflow.
- List Sources. If this skill is used, ensure this is mentioned in the
output AND list the URLs of all papers that were used in producing the
output.
Utility Scripts
All commands are subcommands of scripts/europepmc_api.py. Rate limiting and
retries are handled automatically.
1. Search (search)
Search Europe PMC by query. Supports DOI lookup, keyword search, author search,
PMID lookup, and the full
Europe PMC search syntax.
uv run scripts/europepmc_api.py search "DOI:10.1038/s41586-021-03819-2" --output result.json
uv run scripts/europepmc_api.py search "CRISPR cancer" --max_results 5 --output results.json
uv run scripts/europepmc_api.py search "AUTH:Jumper J" --max_results 10 --output results.json
uv run scripts/europepmc_api.py search "EXT_ID:34265844 AND SRC:MED" --output result.json
uv run scripts/europepmc_api.py search "machine learning" \
--sort "CITED desc" --max_results 20 --output results.json
Arguments:
query (str, required) — search query using Europe PMC syntax--output (str, required) — output JSON file path--max_results (int, default 10) — maximum results per page (max 1000)--result_type (str, default core) — core (full metadata) or lite--cursor (str, default *) — cursor mark for pagination; pass the
nextCursorMark value from a previous response to get the next page--sort (str) — sort order, e.g. CITED desc, P_PDATE_D desc
(publication date descending), P_PDATE_D asc
Output: JSON file with three fields:
hitCount (int) — total number of matching articlesnextCursorMark (str) — cursor for next page; empty string if no more pagesresults (list) — array of article metadata objects
Search Syntax Quick Reference:
DOI:10.xxxx/yyyy — look up by DOIEXT_ID:12345678 AND SRC:MED — look up by PMIDAUTH:surname initials — author searchTITLE:keyword — search in title onlyJOURNAL:name — search by journalPUB_YEAR:2024 or (FIRST_PDATE:[2023-01-01 TO 2023-12-31]) — date filterHAS_FT:y — restrict to articles with full text in Europe PMC- Boolean operators:
AND, OR, NOT
Note: OPEN_ACCESS:y is automatically appended to all queries. You do not
need to add it manually.
2. Download PDF (download_pdf)
Download an open-access PDF from Europe PMC by PMCID.
uv run scripts/europepmc_api.py download_pdf PMC8371605 --output alphafold.pdf
Arguments:
pmcid (str, required) — PubMed Central ID (e.g., PMC8371605)--output (str, required) — filepath to save the PDF
Output: Saves the PDF to the specified file. Exits with an error if the
PMCID is not found or the response is not a valid PDF. Whenever you download a
PDF, check the pdf downloaded is not empty or corrupted.
3. Get Full Text (get_fulltext)
Retrieve the full text of an open-access article and save to a file. Returns
plain text (XML tags stripped) by default, or raw XML with --format xml.
uv run scripts/europepmc_api.py get_fulltext PMC8371605 --output fulltext.txt
uv run scripts/europepmc_api.py get_fulltext PMC8371605 --format xml --output fulltext.xml
Arguments:
pmcid (str, required) — PubMed Central ID--output (str, required) — output file path--format (str, default text) — text (plain text) or xml (raw JATS
XML)
Output: Full text written to the specified file. Exits with an error if the
article is not in the Europe PMC open-access subset.
Important: Only articles in the PMC Open Access Subset have full text
available. If retrieval fails, use search to check the isOpenAccess field
and fall back to the abstract.
4. Get Citations (get_citations)
Retrieve articles that cite a given paper.
uv run scripts/europepmc_api.py get_citations MED 34265844 \
--page_size 25 --output citations.json
Arguments:
source (str, required) — source database: MED (PubMed), PMC, PPR
(preprints), PAT (patents)article_id (str, required) — article ID in the source database--output (str, required) — output JSON file path--page (int, default 1) — page number--page_size (int, default 25) — results per page
Output: JSON file with hitCount and citations array.
5. Get References (get_references)
Retrieve the reference list (bibliography) of a given paper.
uv run scripts/europepmc_api.py get_references MED 34265844 \
--page_size 100 --output references.json
Arguments:
source (str, required) — source database: MED, PMC, PPR, PATarticle_id (str, required) — article ID in the source database--output (str, required) — output JSON file path--page (int, default 1) — page number--page_size (int, default 25) — results per page
Output: JSON file with hitCount and references array.
Common Workflows
DOI to PDF
uv run scripts/europepmc_api.py search "DOI:10.1038/s41586-021-03819-2" --output result.json
PMCID=$(jq -r '.results[0].pmcid // empty' result.json)
uv run scripts/europepmc_api.py download_pdf "$PMCID" --output paper.pdf
PMID to Full Text
uv run scripts/europepmc_api.py search "EXT_ID:34265844 AND SRC:MED" --output result.json
PMCID=$(jq -r '.results[0].pmcid // empty' result.json)
uv run scripts/europepmc_api.py get_fulltext "$PMCID" --output fulltext.txt
Citation Graph Traversal
uv run scripts/europepmc_api.py get_citations MED 34265844 --page_size 50 --output citing.json
uv run scripts/europepmc_api.py get_references MED <CITING_PMID> --output refs.json
Search with Pagination
uv run scripts/europepmc_api.py search "CRISPR" --max_results 100 --output page1.json
CURSOR=$(jq -r '.nextCursorMark // empty' page1.json)
uv run scripts/europepmc_api.py search "CRISPR" --max_results 100 --cursor "$CURSOR" --output page2.json
