ARCHIVE-PUBMED(1)

💖 ARCHIVE-PUBMED(1) — bestie edition 💖

okay so this is a page from the NCBI Entrez Direct User's Manual, and it's all about archive-pubmed and its little sibling index-pubmed. if you've ever wanted your very own local copy of PubMed living on your machine, this is the page that tells you how. 🧚✨

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✨ NAME ✨

archive-pubmed, index-pubmed — maintain a local NCBI PubMed archive

like, literally. that's the whole job description. 💅

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🦋 SYNOPSIS 🦋

archive-pubmed [[-]pma2pme|[-]asn[[.]1]] [[-]daily|[-][re]index]
[[-]clean|[-]clear|[-]scrub] [[-]biocoll|[-]extras|[-]bioconcepts
|[-]generifs] [[-]nihocc] [-ftp|-http[s]] [[-path] dir [[-temp|
-work[ing]] dir]]

index-pubmed

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🌸 DESCRIPTION 🌸

archive-pubmed prepares a directory to hold a local PubMed archive, then downloads a full database dump and auxiliary vocabulary data from NCBI's servers, organizes the dump into an rchive(1) trie, and refreshes the versioned records.

so basically: it sets up the folder 🎀, it grabs the whole dump from NCBI 🌈, it files everything into an rchive(1) trie like the organized queen it is 👑, and then it keeps those versioned records fresh. no cap.

index-pubmed is shorthand for archive-pubmed -index, and takes no options.

that's it. that's the whole thing. it's the drive-thru version of archive-pubmed -index. 🍓

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💅 OPTIONS 💅

• [-]pma2pme | [-]asn[[.]1] — Additionally support retrieval in text ASN.1 Pubmed-entry format.

so on top of everything else, you also get to pull records back out in text ASN.1 Pubmed-entry format. extra format, extra slay. ✨

• [-]daily — Additionally produce or update an inverted index.

this one also builds or refreshes an inverted index for you. lowkey essential if you want searching to actually hit. 🔥

• [-][re]index — Fully reindex, complete with an inverted index.

full send. a complete reindex, and yes, the inverted index comes with it. it's giving main character energy. 👑

• [-]clean | [-]clear — Delete Indices contents and Increment files.

wipes out the Indices contents and the Increment files. bye bestie 💀

• [-]scrub — Delete Indices contents, Increment files, and Postings directories.

same as above but it goes further — Indices contents, Increment files, and the Postings directories. the full reset, no crumbs left. 😭

• [-]biocoll | [-]extras | [-]bioconcepts | [-]generifs — Download or update auxiliary BioConcept and GeneRIF data.

grab or refresh the auxiliary BioConcept and GeneRIF data. the little extras that make everything hit different. 💜

• [-]nihocc — Incorporate NIH Open Citation Collection data, downloaded as needed.

folds in NIH Open Citation Collection data, and it downloads whatever it needs along the way. it knows what it wants. 🎀

• -ftp — Download needed data via FTP (default).

the classic route. this is the default, so if you say nothing, this is what you get. ⭐

• -http[s] — Download needed data via HTTPS.

same data, but over HTTPS instead. secure vibes only. 🔒

• [-path] dir — Place the local archive in dir.

tells it where to put your local archive. pick your dir, live your truth. 🦋

• [-temp|-work[ing]] dir — Place intermediate subtrees in dir.

this is where the intermediate subtrees hang out while the magic happens. the backstage area. 🌈

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🌟 ENVIRONMENT 🌟

• EDIRECT_PUBMED_MASTER — Local archive directory to use in the absence of -path. Expected to hold an absolute path; mandatory when not supplying a path on the command line.

this is your fallback archive directory when you don't pass -path. it has to be an absolute path, and honestly, if you're not giving a path on the command line, this one is mandatory. no ifs, no buts. 🙈

• EDIRECT_PUBMED_WORKING — Directory to hold intermediate subtrees in the absence of -temp|-work[ing]. Expected to hold an absolute path. Defaults to the primary local archive directory when not set.

where the intermediate subtrees go when you didn't hand it a -temp|-work[ing] directory. also expected to be an absolute path. if you don't set it at all? it just defaults to the primary local archive directory. it handles itself. 💖

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💜 SEE ALSO 💜

archive-pmc(1), download-ncbi-data(1), download-pubmed(1), edict(1), expand-current(1), fetch-pubmed(1), phrase-search(1), pm-prepare(1), pm-refresh(1), rchive(1), ref2pmid(1), xtract(1).

the whole friend group 🫶 go read them too, iykyk.

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okay that's the page!! this one's from NCBI, dated 2023-03-29, and it's the ARCHIVE-PUBMED(1) page from the NCBI Entrez Direct User's Manual. go build that archive bestie, you're gonna eat 💖✨🎀🦋🌸💅