ARCHIVE-PIDS(1)

archive-pids 💖 the local PubMed / PMC ID map situation

okay bestie so this is archive-pids from the NCBI Entrez Direct User's Manual — yes, the whole manual is called that, and yes, this page is literally just one tool out of a whole little family of them. let's get into it 🫶

✨ NAME ✨

archive-pids — maintain a local NCBI PubMed / PubMed Central ID map. that's the whole job description. it keeps the receipts on which article ID in PubMed maps to which ID in PubMed Central. 💅

🌸 SYNOPSIS 🌸

archive-pids [[-]daily|[-][re]index] [[-]clean|[-]clear|[-]scrub|
[-]scour|[-]scratch|[-]erase] [-ftp|-http[s]]

so you're picking one thing from the first group, optionally one thing from the second group, and then how you wanna download. look at all those synonyms, the author really said "let me give the girlies options" 😭

🦋 DESCRIPTION 🦋

archive-pids gets a directory all set up to hold a map between PubMed's article identifiers and PubMed Central's, then it downloads a full database dump and organizes the whole thing into an rchive(1) trie.

like... it does the setup, it does the fetching, it does the filing. main character behavior fr fr 👑

💖 OPTIONS 💖

• [-]daily — also produce or update an inverted index while you're at it. lil daily refresh energy ✨
• [-][re]index — fully reindex, complete with an inverted index. the deluxe version, no crumbs left behind 💅
• [-]clean | [-]clear | [-]scrub | [-]scour | [-]scratch | [-]erase — delete Scratch directories. six whole ways to say the same thing, pick your fave, they all hit 🧹
• -ftp — download needed data via FTP. this one is the default, iykyk.
• -http[s] — download needed data via HTTPS. for when you want the lil lock icon 🔒

🎀 ENVIRONMENT 🎀

• EDIRECT_LOCAL_ARCHIVE — the local archive directory to use. it's expected to hold an absolute path, so no relative nonsense bestie 🙈
• EDIRECT_LOCAL_WORKING — the directory that holds the intermediate subtrees. also expected to hold an absolute path. if you don't set it, it just defaults to the local archive directory. lowkey convenient 🫶

🌈 SEE ALSO 🌈

the whole friend group showed up:

archive-nihocc(1), archive-nlmnlp(1), archive-nmcds(1), archive-pmc(1), archive-pubmed(1), archive-taxonomy(1), nquire(1), pm-clean(1), pm-prepare(1), pm-setup(1), rchive(1), xfetch(1), xfilter(1), xinfo(1), xlink(1), xsearch(1). xtract(1).

ok one tiny thing — if you're out here deleting things, mind which directory you point EDIRECT_LOCAL_ARCHIVE at, because the clean/clear/scrub/scour/scratch/erase crew is coming for those Scratch directories and they do not miss. 😭

and that's the page, bestie!! brought to you by NCBI, dated 2025-05-26, in the NCBI Entrez Direct User's Manual. go forth and map those IDs, you absolute icon 💜⭐