PHRASE-SEARCH(1)

💖 phrase-search(1) — the NCBI Entrez Direct User's Manual glow-up 💖

okay so bestie, welcome to phrase-search, straight outta the NCBI Entrez Direct User's Manual. this is the one where we go digging through a local PubMed archive that you already indexed. grab a strawberry 🍓, sit down, we're doing Boolean searches together.

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✨ NAME ✨

phrase-search — search an indexed local NCBI PubMed archive 🦋

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🌸 SYNOPSIS 🌸

phrase-search [-h|-help|--help] [-path dir] -count|-counts|-query
|-filter|-link
|-exact|-title|-words|-pairs|-fields|-terms|-totals query...|-convert
dbas type type [key]|-lookup tag theme...

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💅 DESCRIPTION 💅

phrase-search searches an indexed local NCBI PubMed archive — like, the kind you already prepped with index-pubmed(1). that's it, that's the whole vibe. it's giving "i have a search engine at home." 👑

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🎀 OPTIONS 🎀

• -h, -help, --help — prints usage info. the classic "wait how does this work again" button 🙈
• -path dir — search the local archive that lives in dir. tell it where the goods are at 📁
• -count — print terms and counts, merging wildcards. one big tidy tally, no dupe chaos ✨
• -counts — expand wildcards and print individual term counts. every term gets its own moment, no merging here 💫
• -query — search on words or phrases inside Boolean formulas. this is the main character mode 🔥
• -filter — filter piped-in output from a previous query (quite possibly a remote one). yes, you can chain it, we love a pipeline 🫶
• -exact — strict search, for article round-tripping. no fuzz, no guessing, exact only 💅
• -title — exact search, but limited to the indexed title field. titles only, we're being picky 🎯
• -link — follow links by the given tag (e.g. CITED), merging any duplicates. tag 'em and follow 'em 🔗
• -words — combine searches for individual informative words. word by word by word 📝
• -pairs — combine searches for pairs of adjacent informative words. adjacent besties, always together 👯
• -fields, -terms — interpret the query as a field name and list that field's known terms. and if you pass an empty query, it lists the supported fields instead. lowkey a cheat sheet 👀
• -totals — like -fields, but with term counts. same energy, now with numbers 🔢
• query... — what to search for in the modes above. it may contain the standard Boolean operators AND, OR, and NOT, with parentheses as needed for grouping. go feral with the parentheses, it's allowed 🌈
• -convert dbas type type [key] — convert identifiers in the specified database from one type to another. it accepts either a single identifier on the command line, or a newline-delimited list on standard input. 💫

the database (dbas) may be any of:

• mesh — Medline subject headings in general
• chem — MeSH chemicals
• disz — MeSH diseases
• gene — Genes

and the type may be any of:

• Name — official name
• Code — internal identifier
• Tree — path within MeSH tree (except for gene)
• Desc — description (only for gene)
• Term — synonym (except for gene)

not me clocking that Tree and Term don't do gene, and Desc is gene-only. read the fine print bestie, it's right there 💀

• -lookup tag theme... — look up cross references between internal identifiers read from standard input, where tag identifies a pair of databases (e.g., chdi for chemicals and diseases) and theme... are theme codes of particular interest (with p and m standing in for + and - respectively). 🧚

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🌈 ENVIRONMENT 🌈

• EDIRECT_PUBMED_MASTER — the local archive directory to use in the absence of -path/-master. it's expected to hold an absolute path, and it's mandatory when you're not supplying a path on the command line. no path, no search, periodt. 👑

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🦋 SEE ALSO 🦋

cit2pmid(1), download-ncbi-data(1), edict(1), fetch-pubmed(1), filter-stop-words(1), index-pubmed(1), rchive(1), theme-aliases(1), word-at-a-time(1), xtract(1).

go read the whole friend group, they all slay 💜

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NCBI · 2023-02-21 — mwah, that's the version and date bestie, this page is officially closed out. stay indexed, stay iconic, iykyk 💖✨🎀