CIT2PMID(1)

💖 CIT2PMID(1) 💖

okay bestie, gather round, because this is a page from the NCBI Entrez Direct User's Manual and it's about a little tool called cit2pmid. she's giving matchmaker energy: you hand her a citation, she goes hunting for the NCBI PubMed identifiers that belong to it. no cap. ✨

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🌸 NAME 🌸

cit2pmid — the way she finds candidate NCBI PubMed identifiers for a citation. literally her whole job. 💅

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🦋 SYNOPSIS 🦋

cit2pmid [-debug] [-strict] [-remote|-eutils|-local|-exact|-verify]
[-asn file|-cit file] [-title|-TITL str] [-author|-FAUT|-LAUT str]
[-journal|-JOUR str] [-year|-YEAR|-PDAT str] [-volume|-VOL str]
[-issue|-ISS str] [-page[s]|-PAGE str]

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✨ DESCRIPTION ✨

so cit2pmid tries to identify NCBI PubMed identifiers that correspond to a citation you supply. that's it, that's the mission. 🎯

and some of her modes go dig through an indexed local NCBI PubMed archive — you know, the kind of thing that gets prepared by archive-pubmed(1). so if you've got one of those lying around, she can do her little search in-house. 🏠💖

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👑 OPTIONS 👑

here's the whole menu, bestie, no skipping, every single one:

• -debug — trace some aspects of execution. she'll show you the receipts of what she's doing. 🔍
• -strict — do stricter matching. heads up though: this one only works in -local mode, at least for now. 🫠
• -remote — use the nquire -citmatch remote service. this is the default, so if you don't say anything, this is what you get. 🌈
• -eutils — use the esearch remote service instead.
• -local — use transmute -r2p (ref2pmid) for a relaxed search against the local archive. 🏡
• -exact — use xsearch -exact for strict matching against the local archive. precision queen. 🎯
• -verify — query against the local archive with strict (but not -exact) matching, then confirm the positive candidates via citmatch. double-checking the vibes. ✅
• -asn file — read NCBI Pub ASN.1 from file (- means standard input). ⚠️ this must be the only query specification. like, she's not taking other orders when you do this.
• -cit file — read CITATION XML from file (- means standard input). ⚠️ also must be the only query specification. same rule, different format.
• -title, -TITL str — the article title. ngl, you may need other fields to disambiguate, especially if it's incomplete. 📝
• -author str — author name (last name, optionally followed by initials). this one may appear twice, for first and last authors. (otherwise, she just takes it to be the first author only.) 👯
• -FAUT str — explicitly name the first author. no guessing. 🥇
• -LAUT str — explicitly name the last author. 🏁
• -journal, -JOUR str — journal name. 📚
• -year, -YEAR, -PDAT str — publication year. 🗓️
• -volume, -VOL str — journal volume. 📖
• -issue, -ISS str — journal issue. 🗂️
• -page[s], -PAGE str — journal page, or a hyphenated range. 📄

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🧚 ENVIRONMENT 🧚

she reads these little environmental cues, iykyk:

• EDIRECT_LOCAL_ARCHIVE — the local archive directory to use. she expects it to hold an absolute path, and it's mandatory for any mode besides -remote and -eutils. so if you're going local, you need this. 💀
• EDIRECT_LOCAL_WORKING — the directory to hold intermediate subtrees; also expected to hold an absolute path. when it's not set, it defaults to the local archive directory. 🫶

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🎀 SEE ALSO 🎀

go read these too, bestie, they're all part of the fam: archive-pubmed(1), ecollect(1), edict(1), esearch(1), nquire(1), ref2pmid(1), transmute(1), xfetch(1), xlink(1), xsearch(1).

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and that's the whole page, periodt. 💜 this edition came from NCBI, dated 2025-05-26 — so when you cite her, you know exactly which version of the vibe you're working with. slay, go find those PMIDs. 💅✨🦋