xy-pubmed-pdf-downloader_skill

Overview

This skill downloads open-access PDF articles from PubMed Central (PMC) and Europe PMC using identifiers like PMC ID, PubMed URL, PMID, or DOI. It supports both single-file and batch download modes, with automatic fallbacks and optional output naming and directory controls.

How this skill works

Provide a PMC identifier, PubMed URL, PMID, or DOI and the script extracts or converts the identifier to locate the PDF on PMC. If the PMC download fails, the tool automatically falls back to Europe PMC. Batch mode reads a plaintext list of identifiers and downloads each file with a configurable delay to reduce server load.

When to use it

• You need a PDF for an open-access article hosted on PubMed Central or Europe PMC.
• You have a DOI, PubMed URL, PMC ID, or PMID and want an automated download command.
• You need to download many open-access articles in bulk without manual clicking.
• You want predictable filenames and an organized output directory for archived papers.

Best practices

• Confirm the target articles are open-access on PMC before attempting downloads.
• Use batch mode with the default delay to avoid overloading upstream servers.
• Specify an output directory to keep downloads organized and avoid cluttering the working folder.
• Install and update the requests library (pip install requests) to ensure network reliability.
• Validate DOIs first if conversion to PMC IDs is required; handle conversion failures gracefully.

Example use cases

• Download a single article by PMC ID: python3 scripts/download_pmc_pdf.py PMC12867338
• Fetch a PDF from a PubMed URL or DOI when you only have a link or citation.
• Archive a list of open-access papers for a literature review using batch mode and an id list file.
• Rename and store PDFs in a project folder using the filename and output directory options.