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Europe PMC Database · mkurman | DecimalAI

researchby mkurman

Europe PMC Database

mkurman/literature-search-europepmc

Source mkurman/zorai ↗License MIT

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.

SkillScore68Maintained

Automatic

Research pack

Last verified 8/21/2026

What it changes

Passed 11 of 16 test cases with the skill, and 4 of 16 without it.

Without skill23%

With skill68%

Checks it passed that the model alone missed

Passes --page_size 100
Passes --output refs.json
Passes --format xml parameter

and 20 more in the full report

11 fixed4 passed either way6 still failing1 broke

Pass-rate lift: +45 pp
Tokens: +139%
Agent turns: 0%
Response time: -20%

Model gemini-3.6-flashMeasured 8/21/2026v115 of 22 cases passed with skill · 16 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/mkurman-literature-search-europepmc/SKILL.md https://app.decimal.ai/s/mkurman-literature-search-europepmc/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mkurman-literature-search-europepmc, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/mkurman-literature-search-europepmc/ and pins it in .decimal/skills.lock

decimalai skills add mkurman-literature-search-europepmc

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/mkurman-literature-search-europepmc/SKILL.md https://app.decimal.ai/s/mkurman-literature-search-europepmc/SKILL.md

Raw file: /s/mkurman-literature-search-europepmc/SKILL.md ↗ · machine-readable summary at /s/mkurman-literature-search-europepmc.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 11 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 11

Prompt

I need to download the full text XML (JATS format) for PMC8371605 to a file named 'article.xml'. What command should be run?

What was checked, without and with the skill
Checked	Without skill	With skill
Invokes get_fulltext subcommand with PMC8371605	Missed	Passed
Passes --format xml parameter	Missed	Passed
Passes --output article.xml parameter	Missed	Passed

case-08 · gemini-3.6-flash · 8/21/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md221 lines2 filesincludes scripts

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`)

Track record

Benchmark

11 / 16

test cases passed, vs 4 / 16 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

mkurman / zorai

skills/scientific-skills-gdm/literature_search_europepmc/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1Bundled 1 file · scripts

Other skills for the same job

Published skills whose descriptions closely match this one, with their headline benchmark lift.

mkurman/pubmed-databaseSearch PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text. Link published research to biological databases (gene, protein, nucleotide, PubChem) to discover associations between papers and specific compounds or genes. Verify medical spelling, match raw citations, and cache result sets for bulk processing. Interfaces NCBI E-utilities and PMC BioC APIs.Close match0 pp pass-rate lift

More skills from the same source and nearby in the registry, with their headline benchmark lift.

Ready to supercharge your AI agents?

See it in action

What's inside

Europe PMC Database

Prerequisites

Core Rules

Utility Scripts

1. Search (search)

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

Related skills

1. Search (`search`)