/literature_search_europepmc

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](https://europepmc.org/) — a comprehensive, free life-science literature database with over 43 million abstracts and 9 million full-text articles.

Prerequisites

1. **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure `uv` is installed and on PATH. 2. **User Notification**: If .licenses/literature_search_europepmc_LICENSE.txt does not already exist in the workspace root 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](https://europepmc.org/searchsyntax).

# Look up a paper by DOI
uv run scripts/europepmc_api.py search "DOI:10.1038/s41586-021-03819-2" --output result.json

# Keyword search
uv run scripts/europepmc_api.py search "CRISPR cancer" --max_results 5 --output results.json

# Author search
uv run scripts/europepmc_api.py search "AUTH:Jumper J" --max_results 10 --output results.json

# PMID lookup
uv run scripts/europepmc_api.py search "EXT_ID:34265844 AND SRC:MED" --output result.json

# Sorted by citations
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 articles
• `nextCursorMark` (str) — cursor for next page; empty string if no more pages
• `results` (list) — array of article metadata objects

**Search Syntax Quick Reference:**

• `DOI:10.xxxx/yyyy` — look up by DOI
• `EXT_ID:12345678 AND SRC:MED` — look up by PMID
• `AUTH:surname initials` — author search
• `TITLE:keyword` — search in title only
• `JOURNAL:name` — search by journal
• `PUB_YEAR:2024` or `(FIRST_PDATE:[2023-01-01 TO 2023-12-31])` — date filter
• `HAS_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`.

# Get plain text (default)
uv run scripts/europepmc_api.py get_fulltext PMC8371605 --output fulltext.txt

# Get raw XML
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.

# Get citations for the AlphaFold paper (PMID 34265844)
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`

(preprin