skills.rest
carmonalab
carmonalabOFFICIAL
Explore all skills by this author →
Website𝕏@carmonationGitHub

literature-search-europepmc

Search Europe PMC and download open-access full texts, PDFs, citations, and references.

1|Updated Mar 7, 2025
Search Tags:#bibliography#citations#full text#literature search#open access#pdf download#europe pmc
One-click install
npx skills add https://github.com/carmonalab/ECODA_paper --skill literature-search-europepmc-carmonalab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: literature-search-europepmc
Source: https://github.com/carmonalab/ECODA_paper/tree/main/.agents/skills/literature_search_europepmc
Command: npx skills add https://github.com/carmonalab/ECODA_paper --skill literature-search-europepmc-carmonalab

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires polite-http, and includes scripts (resource) components.

What problem does it solve? Finding and retrieving open-access scientific literature manually is slow and fragmented across publisher sites. This Skill provides programmatic access to Europe PMC's database of over 43 million abstracts and 9 million full-text articles, letting you search, download, and explore papers directly from the command line. ## Core Features & Use Cases - Literature Search: Query Europe PMC by DOI, PMID, author, keyword, journal, or date range using the full Europe PMC search syntax, with automatic open-access filtering and cursor-based pagination. - Full-Text & PDF Retrieval: Download open-access PDFs or extract full text as plain text or raw JATS XML by PMCID. - Citation Graph Exploration: Retrieve the articles citing a given paper or fetch its complete reference list for bibliography analysis. - Use Case: Given a DOI of a landmark paper, look up its PMCID, download the PDF, pull the full text for review, and then traverse its citing articles to map the surrounding research landscape. ## Quick Start Search Europe PMC for open-access papers on CRISPR cancer and save the top five results to a JSON file.

Frequently Asked Questions about literature-search-europepmc

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I search Europe PMC for papers by DOI or keyword?▼

Run the search subcommand with a query like "DOI:10.1038/s41586-021-03819-2" or a keyword phrase such as "CRISPR cancer". Results are written to a JSON file specified with --output, and OPEN_ACCESS:y is appended automatically to every query.

How to download an open-access PDF from Europe PMC by PMCID?▼

Use the download_pdf subcommand with the PMCID, for example "uv run scripts/europepmc_api.py download_pdf PMC8371605 --output paper.pdf". The script validates that the response is a real PDF and exits with an error if the article is not open access.

Can I get full text for any article in Europe PMC?▼

Full text is only available for articles in the PMC Open Access Subset. If get_fulltext fails, run a search first to check the isOpenAccess field and fall back to the abstract when full text is unavailable.

How do I find papers that cite a specific article?▼

Use the get_citations subcommand with the source database and article ID, such as "get_citations MED 34265844". The output JSON contains a hitCount and a citations array, with pagination controlled by --page and --page_size.

Why does the skill restrict results to open-access articles?▼

The script automatically appends OPEN_ACCESS:y to every query so that retrieved content can be legally downloaded and reused. This filter cannot be removed or overridden, ensuring only freely accessible literature is returned.

Related Skills

Explore More Education & Research Skills→
Estrella-231Estrella-231

paper-lookup

Search academic databases via REST APIs and return raw JSON results.

Community
Advanced
dy9759dy9759

literature-reader

Extract metadata and summarize academic PDFs into structured Markdown notes.

Community
Intermediate
xqinagxqinag

openalex

Search OpenAlex for citation data, affiliations, and funding information.

Community
Intermediate
tassiovaletassiovale
13

citation-management

Search academic databases, extract metadata, and generate BibTeX entries.

Community
Advanced