FETCH-PUBMED(1)

📦
version 19.2.20230331 · 2 versions
, in debian bookworm, ubuntu noble

💖 FETCH-PUBMED(1) 💖

okay bestie, welcome to the NCBI Entrez Direct User's Manual page for fetch-pubmed, and no cap, this one is a whole vibe 🌸

✨ NAME ✨

fetch-pubmed — grab records out of a local NCBI PubMed archive, picked by UID 🎀

🦋 SYNOPSIS 🦋

fetch-pubmed [-strict|-mixed] [[-path] dir] [-all] [-fresh]
[-asn|-xml|-pme] [-turbo]

🌈 DESCRIPTION 🌈

so here's the tea 🍓: fetch-pubmed reads a list of record IDs from standard input and prints the matching bits of a local NCBI PubMed archive — one that was made by archive-pubmed(1) — out to standard output.

and like, why would you do that? because you're probably gonna feed it to xtract(1) or something similar next. it's giving pipeline main character energy 👑

💅 OPTIONS 💅

  • -strict|-mixed — runs rchive(1) with -flag strict or -flag mixed, respectively. pick your fighter ✨
  • [-path] dir — use the local archive that lives in dir. lowkey the path is optional-looking but dir is what matters 🫶
  • -all — dump the ENTIRE archive. all of it. not a crumb left behind 😭
  • -fresh — dump the entire archive into filenames shaped like pubmed001.xml.gz, and it uses any already-existing files like that as a starting point 🌱
  • -asn — retrieve ASN.1 ⭐
  • -xml — retrieve XML. this is the default btw, iykyk 💚
  • -pme — produce ASN.1 on the fly, via pma2pme 🧚
  • -turbo — adds NEXT_RECORD_SIZE nodes so navigation goes zoom zoom 🔥

👑 ENVIRONMENT 👑

  • EDIRECT_PUBMED_MASTER — the local archive directory to use when you didn't pass -path. it's expected to hold an absolute path, and it is mandatory when you're not supplying a path on the command line. no path, no archive, no records — periodt 💀

🎀 SEE ALSO 🎀

archive-pubmed(1), cit2pmid(1), ds2pme(1), edict(1), phrase-search(1), pma2pme(1), rchive(1), stream-pubmed(1), xtract(1).

the whole friend group, obsessed with them fr fr 💜

ngl, if you skipped the env var and skipped the path too, that's on you bestie 🙈 set EDIRECT_PUBMED_MASTER or pass dir, one of the two, okay?

and that's the page!! brought to you by NCBI, dated 2023-02-20, and it's the FETCH-PUBMED(1) manual page from the NCBI Entrez Direct User's Manual. slay, go fetch those records 💖✨🌸

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