DOWNLOAD-PUBMED(1)

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version 24.0.20250523 · 3 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 DOWNLOAD-PUBMED 💖

okay bestie, so this one is from the NCBI Entrez Direct User's Manual — yeah, that Entrez Direct, the toolkit that lives on your machine and does your bioinformatics bidding. and this page? this page is about download-pubmed, which does literally exactly what it says on the tin. no plot twist. we love a consistent queen. 👑

✨ NAME ✨

download-pubmed — download an NCBI PubMed archive dump

like. the whole entire archive. to your current directory. slay.

🎀 SYNOPSIS 🎀

download-pubmed [-ftp|-http[s]] [section...]

that's it. that's the whole vibe. optional transport flag, optional list of sections, go. 🦋

🌸 DESCRIPTION 🌸

so here's the tea: download-pubmed downloads one or more sections of NCBI's PubMed archive, and it drops them right into your current directory. no drama, no config file, no "please edit this YAML first" nonsense. it just goes and gets them. 💅

and if you run it with no arguments at all? then it does the maximalist thing and downloads the baseline and updatefiles sections for you. both of them. unprompted. main character energy fr fr.

💡 pro tip from the manpage itself: it's sections of the archive we're talking about, so if you only want a slice, just say which slice. otherwise you're getting the whole cake.

⭐ OPTIONS ⭐

  • -ftp — downloads via FTP. and yes, this is the default, so if you're not specifying anything, you're already FTP-ing. it's giving "the status quo is FTP". 🌈
  • -http[s] — downloads via HTTPS. same job, different transport. pick your fighter. 🥊
  • section... — the archive section(s) you want to download. one, or several, or none (in which case, see above — baseline and updatefiles come to the party uninvited). ✨

👑 SEE ALSO 👑

the whole friend group, all of them iconic, all of them linked:

go read them. iykyk. 🫶

okay that's the whole page, you ate it, no crumbs. this was NCBI's DOWNLOAD-PUBMED(1), dated 2025-05-26, part of the Entrez Direct user's manual. go download some archives bestie, you've got this. 💜🧚💖

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