ARCHIVE-TAXONOMY(1)

💖 archive-taxonomy — bestie's guide to keeping a local NCBI taxonomy archive 💖

okay so this page lives in the NCBI Entrez Direct User's Manual (that's the manual name, iykyk), and it's all about archive-taxonomy. buckle up 🎀

✨ NAME ✨

archive-taxonomy — maintain a local NCBI taxonomy archive

🌸 SYNOPSIS 🌸

archive-taxonomy [[-]daily|[-][re]index] [[-]clean|[-]clear|[-]scrub|
[-]scour|[-]erase|[-]zap] [-info] [-ftp|-http[s]]

🦋 DESCRIPTION 🦋

so archive-taxonomy is literally the girlboss that sets up a directory to hold a local taxonomy archive. step one: it preps that directory. step two: it downloads a full database dump from NCBI's servers. step three: it organizes the dump into an rchive(1) trie. step four: it refreshes the versioned records. that's the whole glow-up pipeline, no cap ✨

💅 OPTIONS 💅

• [-]daily — additionally produce or update an inverted index. lil daily touch-up energy 🫶
• [-][re]index — fully reindex, complete with an inverted index. the full reset, the whole shebang.
• [-]clean | [-]clear — delete Indices contents and Increment files.
• [-]scrub — delete Indices contents, Increment files, and Postings directories. deeper clean bestie 🧼
• [-]scour — delete Indices contents, Increment files, and Postings, Data, Archive, and Sentinel directories.
• [-]erase — delete Indices contents, Increment files, Postings, Data, Archive, and Sentinel directories, and Extras directory contents. yeah she's taking everything 😭
• [-]zap — delete the entire archive. ⚡ poof. gone. iconic but devastating.
• -info — check whether the archive is complete and up to date, and report what's wrong if it isn't. it's giving vibe check 👑
• -ftp — download needed data via FTP (this is the default).
• -http[s] — download needed data via HTTPS.
• [-path] dir — place the local archive in dir.
• [-temp|-work[ing]] dir — place intermediate subtrees in dir.

🌈 ENVIRONMENT 🌈

• EDIRECT_LOCAL_ARCHIVE — local archive directory to use; expected to hold an absolute path.
• EDIRECT_LOCAL_WORKING — directory to hold intermediate subtrees; expected to hold an absolute path. when it's not set, it defaults to the local archive directory. defaults are so comforting fr fr 💜

💖 SEE ALSO 💖

archive-nihocc(1), archive-nlmnlp(1), archive-nmcds(1), archive-pids(1), archive-pmc(1), archive-pubmed(1), download-ncbi-data(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).

and that's the whole page bestie!! 🎀 this one's from NCBI, dated 2025-05-26 — so go forth, archive your taxonomy, and slay 💅✨