Preprint Search on bioRxiv
LigphiDonk/Oh-my--paper
Searches bioRxiv life sciences preprints by keyword, author, date range or category with a Python script, returning JSON metadata and optional PDF downloads.
Search Europe PMC for scientific literature and download open-access full texts and PDFs.
Install Literature Search Europepmc
$ npx skills add google-deepmind/science-skills --skill literature-search-europepmc -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install google-deepmind/science-skills literature-search-europepmc --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/literature_search_europepmc .claude/skills/literature-search-europepmc && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "literature-search-europepmc" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/literature_search_europepmc into .claude/skills/literature-search-europepmc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-search-europepmc", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/google-deepmind/science-skills/tree/main/skills/literature_search_europepmcType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add google-deepmind/science-skills --skill literature-search-europepmc -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install google-deepmind/science-skills literature-search-europepmc --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/literature_search_europepmc .agents/skills/literature-search-europepmc && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "literature-search-europepmc" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/literature_search_europepmc into .agents/skills/literature-search-europepmc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-search-europepmc", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add google-deepmind/science-skills --skill literature-search-europepmc -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install google-deepmind/science-skills literature-search-europepmc --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/literature_search_europepmc .cursor/skills/literature-search-europepmc && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "literature-search-europepmc" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/literature_search_europepmc into .cursor/skills/literature-search-europepmc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-search-europepmc", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/google-deepmind/science-skills.git --path skills/literature_search_europepmc--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add google-deepmind/science-skills --skill literature-search-europepmc -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install google-deepmind/science-skills literature-search-europepmc --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/literature_search_europepmc .gemini/skills/literature-search-europepmc && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "literature-search-europepmc" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/literature_search_europepmc into .gemini/skills/literature-search-europepmc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-search-europepmc", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install google-deepmind/science-skills literature-search-europepmcInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add google-deepmind/science-skills --skill literature-search-europepmc -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/literature_search_europepmc .github/skills/literature-search-europepmc && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "literature-search-europepmc" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/literature_search_europepmc into .github/skills/literature-search-europepmc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-search-europepmc", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add google-deepmind/science-skills --skill literature-search-europepmc -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install google-deepmind/science-skills literature-search-europepmc --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/literature_search_europepmc .opencode/skills/literature-search-europepmc && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "literature-search-europepmc" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/literature_search_europepmc into .opencode/skills/literature-search-europepmc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-search-europepmc", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
literature-search-europepmc- GitHub stars
- 3.2k
- Used in
- 2 other repos
- Token cost
- ~2.1k tokens
- SKILL.md length
- 753 words
- Files
- 3 (incl. scripts, references)
- Skills in repo
- 40
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Search Europe PMC for scientific literature and download open-access full texts and PDFs.
- Works in 5 steps: Search (search) → Download PDF (download_pdf) → Get Full Text (get_fulltext) → …
- Tasks that involve Citation management
- SKILL.md covers Prerequisites, Core Rules, Utility Scripts and Common Workflows
- Runs Python scripts from its folder; calls uv and jq
What it does
Literature Search Europepmc is an agent skill from google-deepmind/science-skills. 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.
Its SKILL.md is about 2.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files, including scripts and reference files (for example `scripts/europepmc_api.py`).
It sits in Research & Science, covering Citation management and Literature review. It works with Python. The repository describes itself as: GDM Science Skills to speed up agentic scientific workflows with better grounding and higher token efficiency. Integrate insights from AlphaGenome, AFDB, UniProt and 30+ other… The licence is Apache-2.0.
When your agent uses it
- Tasks that involve Citation management
- Tasks that involve Literature review
Example prompts
- “/literature-search-europepmc”
Requirements
- Python 3
Workflow steps
5 steps, taken from the step headings in SKILL.md.
What it can do on your machine
Read from SKILL.md and the folder at commit 8ab7672. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
uvjq
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
europepmc.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Literature Search Europepmc loads about 2.1k tokens when it runs, and up to ~2.6k if it reads all its reference files. Until then it costs about 50 tokens; SKILL.md has 753 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
The full file from google-deepmind/science-skills at commit 8ab7672, republished under its Apache-2.0 licence (© google-deepmind). 753 words, ~2,074 tokens.
Download SKILL.mdSave it as
.claude/skills/literature-search-europepmc/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.- 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 theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.- 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:yto 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
--outputto 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.
# 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.jsonArguments:
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, defaultcore) —core(full metadata) orlite--cursor(str, default*) — cursor mark for pagination; pass thenextCursorMarkvalue 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:2024or(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:yis automatically appended to all queries. You do not need to add it manually.
Show full SKILL.md (315 more words)Show less
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.pdfArguments:
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.xmlArguments:
pmcid(str, required) — PubMed Central ID--output(str, required) — output file path--format(str, defaulttext) —text(plain text) orxml(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
searchto check theisOpenAccessfield 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.jsonArguments:
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.
# Get references from the AlphaFold paper
uv run scripts/europepmc_api.py get_references MED 34265844 \
--page_size 100 --output references.jsonArguments:
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
# Step 1: Search for the PMCID
uv run scripts/europepmc_api.py search "DOI:10.1038/s41586-021-03819-2" --output result.json
PMCID=$(jq -r '.results[0].pmcid // empty' result.json)
# Step 2: Download the PDF
uv run scripts/europepmc_api.py download_pdf "$PMCID" --output paper.pdfPMID to Full Text
# Step 1: Find the PMCID from a PMID
uv run scripts/europepmc_api.py search "EXT_ID:34265844 AND SRC:MED" --output result.json
PMCID=$(jq -r '.results[0].pmcid // empty' result.json)
# Step 2: Get the full text
uv run scripts/europepmc_api.py get_fulltext "$PMCID" --output fulltext.txtCitation Graph Traversal
# Find what papers cite a landmark study, then check their references
uv run scripts/europepmc_api.py get_citations MED 34265844 --page_size 50 --output citing.json
# Parse a cited paper's PMID and explore its references
uv run scripts/europepmc_api.py get_references MED <CITING_PMID> --output refs.jsonSearch with Pagination
# First page
uv run scripts/europepmc_api.py search "CRISPR" --max_results 100 --output page1.json
# Extract cursor for next page
CURSOR=$(jq -r '.nextCursorMark // empty' page1.json)
# Next page
uv run scripts/europepmc_api.py search "CRISPR" --max_results 100 --cursor "$CURSOR" --output page2.json© google-deepmind, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 2 other files (scripts, references) in skills/literature_search_europepmc of google-deepmind/science-skills.
- SKILL.md
- references/citation.bib
- scripts/europepmc_api.py
Open the folder on GitHubat commit 8ab7672
Used in 2 other repositories
We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in google-deepmind/science-skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Literature Search Europepmc next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Literature Search Europepmc this skillgoogle-deepmind/science-skills | 3.2k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Preprint Search on bioRxivLigphiDonk/Oh-my--paper | 739 | 12 repos | ~3.7k | Automated safety check: Pass | MIT | |
| Paper Research on arXivXiaomiMiMo/MiMo-Code | 14k | — | ~1.5k | Automated safety check: Pass | MIT | |
| NSFC Literature Review WriterHuiyuLi-2000/Chinese-Grant-Writer-Skills | 439 | 1 repos | ~1.4k | Automated safety check: Notes | MIT | |
| Autonomous Researchfedericodeponte/opendraft | 507 | — | ~8.2k | Automated safety check: Pass | Apache-2.0 | |
| Literature Reviewer Skillstephenlzc/AI-Powered-Literature-Review-Skills | 175 | 1 repos | ~4.5k | Automated safety check: Pass | MIT |
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NSFC Literature Review Writer
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Writes the research-status literature review and critique section of an NSFC grant proposal, backed by a bundled multi-source literature search.
Autonomous Research
federicodeponte/opendraft
An 18-agent pipeline that turns one topic line into a drafted research paper, literature review, or thesis chapter.
Literature Reviewer Skill
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根据用户提供的论文主题，进行系统性中英文文献回顾（Literature Survey）. An agent skill from stephenlzc/AI-Powered-Literature-Review-Skills.
Arxiv MCP Server
blazickjp/arxiv-mcp-server
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Related
Works with
Categories
Questions about Literature Search Europepmc
What does Literature Search Europepmc do?
Search Europe PMC for scientific literature and download open-access full texts and PDFs. Literature Search Europepmc is an agent skill from google-deepmind/science-skills. Search Europe PMC for scientific literature and download open-access full texts and PDFs.
When should I use Literature Search Europepmc?
Literature Search Europepmc fits situations like: tasks that involve Citation management; tasks that involve Literature review.
How do I install Literature Search Europepmc in Claude Code?
Run `npx skills add google-deepmind/science-skills --skill literature-search-europepmc -a claude-code`. Or copy the skill folder (skills/literature_search_europepmc in google-deepmind/science-skills) into .claude/skills/literature-search-europepmc in your project. Claude Code loads it when a task matches its description.
How do I install Literature Search Europepmc in Codex?
Run `npx skills add google-deepmind/science-skills --skill literature-search-europepmc -a codex`. Or copy the skill folder (skills/literature_search_europepmc in google-deepmind/science-skills) into .agents/skills/literature-search-europepmc in your project. Codex loads it when a task matches its description.
Can I use Literature Search Europepmc in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add google-deepmind/science-skills --skill literature-search-europepmc -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/literature-search-europepmc, .gemini/skills/literature-search-europepmc, .github/skills/literature-search-europepmc and .opencode/skills/literature-search-europepmc in your project.
What does Literature Search Europepmc need to run?
Going by SKILL.md and its folder, Literature Search Europepmc needs Python for the scripts in its folder and the command-line tools its instructions call (uv and jq). Our summary lists: Python 3.
Does Literature Search Europepmc access the network?
SKILL.md names 1 domain. As links in the text: europepmc.org. This is read from the text; nothing was executed.
Is Literature Search Europepmc safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Literature Search Europepmc use?
Literature Search Europepmc is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Literature Search Europepmc use?
About 2.1k tokens (SKILL.md is roughly 8.3k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 506 tokens, read only when the agent opens those files.
What are the alternatives to Literature Search Europepmc?
Skills that share tags, products or a category with Literature Search Europepmc: Preprint Search on bioRxiv (LigphiDonk/Oh-my--paper, 739 stars), Paper Research on arXiv (XiaomiMiMo/MiMo-Code, 14k stars), NSFC Literature Review Writer (HuiyuLi-2000/Chinese-Grant-Writer-Skills, 439 stars) and Autonomous Research (federicodeponte/opendraft, 507 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Literature Search Europepmc?
google-deepmind (a GitHub organization) maintains it in google-deepmind/science-skills, which has 3,233 GitHub stars. The repository holds 40 skills in this directory. The repository was last updated on October 9, 2026.
Source: google-deepmind/science-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.