Literature Search Europepmc
Search open-access life-science papers on Europe PMC and pull citations or full text without hand-rolling API filters or rate limits.
Overview
Literature Search Europe PMC is an agent skill for the Idea phase that searches open-access life-science literature and downloads full texts and citations via the Europe PMC wrapper script.
Install
npx skills add https://github.com/google-deepmind/science-skills --skill literature-search-europepmcWhat is this skill?
- Targets Europe PMC with 43M+ abstracts and 9M+ full-text open-access articles
- Enforces OPEN_ACCESS:y on every query so results stay openly usable
- Uses the bundled wrapper script—not raw API calls—for rate limits and deps
- Retrieves full-text XML/plain text by PMCID plus citation lists
- Requires one-time LICENSE_NOTIFICATION.txt user acknowledgment per skill dir
- 43+ million abstracts
- 9+ million full-text articles
- OPEN_ACCESS:y enforced on every search
Adoption & trust: 642 installs on skills.sh; 1.7k GitHub stars; 3/3 security scanners passed (skills.sh audits).
What problem does it solve?
You need citable papers and full-text excerpts from Europe PMC but lack a safe, rate-aware path that stays open-access only.
Who is it for?
Builders doing biomed, health, or science-adjacent ideation who must pull OA papers and bibliographies through one guarded script.
Skip if: Paywalled journal access, legal advice on reuse, or workflows that require removing the mandatory open-access query filter.
When should I use this skill?
You need to search Europe PMC for open-access scientific literature, download full texts or PDFs by PMCID, or pull citation lists.
What do I get? / Deliverables
You get filtered search results, PMCID-linked full text or PDFs where available, and citation lists ready for memos, specs, or validation notes.
- Search result sets (open access only)
- Downloaded full-text XML/plain text or PDFs by PMCID
- Citation and bibliography lists
Recommended Skills
Journey fit
Literature discovery belongs in Idea because it supports opportunity and evidence gathering before you commit to a product direction. Research is the shelf for external papers, PMCIDs, and bibliographies that inform what to build or validate.
How it compares
Open-access Europe PMC retrieval skill with a fixed wrapper—not a general web scraper or non-OA literature aggregator.
Common Questions / FAQ
Who is literature-search-europepmc for?
Solo builders and agent users researching life-science topics who want Europe PMC open-access search and downloads with dependency-safe scripting.
When should I use literature-search-europepmc?
Use it in Idea while researching competitors, mechanisms, or evidence—before Validate—when you need papers, PMC full text, or citation graphs from Europe PMC only.
Is literature-search-europepmc safe to install?
It runs network-backed scripts and writes license notification files; check Europe PMC terms, verify `uv` setup, and read the Security Audits panel on this Prism page.
SKILL.md
READMESKILL.md - Literature Search Europepmc
# 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 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](https://europepmc.org/searchsyntax). ```bash # 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`,