EDIRECT(1)

👑 EDIRECT — access NCBI Entrez from the command line (DEPRECATED)

okay so bestie, welcome to the NCBI Entrez Direct User's Manual page for edirect. Yes it's giving "legacy icon" energy, yes it says DEPRECATED right in the name, and yes we're still gonna read the whole thing together because that's what besties do 💖

✨ SYNOPSIS ✨

like, here's the whole vibe, one form per line:

edirect -version

esearch (edirect -search) options

elink (edirect -link) options

efilter (edirect -filter) options

esummary (edirect -summary) options

efetch (edirect -fetch) options

einfo (edirect -info) options

epost (edirect -post) options

espell (edirect -spell) options

ecitmatch (edirect -citmatch) options

eproxy (edirect -proxy) options

econtact (edirect -contact) options

enotify (edirect -notify) options

eaddress (edirect -address) options

eblast (edirect -blast) options

ftp-ls (edirect -ftpls) options

ftp-cp (edirect -ftpcp) options

transmute (edirect -tmute) options

edirect -nquir options

that's a LOT of options, and honestly? slay. she's versatile 💅

🌸 DESCRIPTION 🌸

Note: edirect might not appear in future releases of NCBI Entrez Direct. However, several individual commands (esearch through epost) live on as nquire-based shell scripts.

not me reading "might not appear in future releases" and feeling a little 😭. But it's fine!! because the individual commands esearch through epost are still out here living their best lives as nquire-based shell scripts. main character energy, periodt.

So edirect (aka Entrez Direct) is a command-line utility for consulting NCBI's set of interconnected databases — like publication, sequence, structure, gene, variation, expression, etc. — in a whole variety of fashions. Most of those fashions are documented individually in their own dedicated man pages (iykyk, go read those too 🫶). The one exception is edirect -nquir, which roughly corresponds to nquire but is fully independent — she's her own girl, no cap.

🎀 COMMON OPTIONS 🎀

Most subcommands accept these, on top of whatever command-specific options they've got going on. The way that every single one of these is listed below, bestie, I would never skip one 🙈

• -help — Print usage information. literally the "help me" button.
• -email address — Send the given e-mail address to have someone to notify in case a runaway script causes problems with an NCBI Entrez server. pls give them a way to reach you if your script goes feral 💀
• -tool name — Send the given client name.
• -http[s] get — Force the use of GET rather than POST HTTPS requests.
• -alias filename — Specify a file of shortcut keywords and query strings or URL sections.
• -silent — Suppress connection failure retry messages.
• -verbose — Display the ENTREZ_DIRECT XML field values at each step.
• -debug — Print the internal URL query and XML results of each step.
• -base URL — Specify a particular server for quality assurance testing.

🦋 ENVIRONMENT 🦋

• EDIRECT_DO_AUTO_ABBREV — Accept (currently) unambiguous truncated option names, as in -verbo for -verbose. lowkey the laziest (affectionate) feature ever and I'm obsessed.
• NCBI_API_KEY — NCBI E-Utilities API key, allowing for a higher request rate at the cost of some anonymity. so like, faster requests but everyone can see it's you. the tradeoff is real 😭

🌈 SEE ALSO 🌈

eaddress(1), eblast(1), ecitmatch(1), econtact(1), efetch(1), efilter(1), einfo(1), elink(1), enotify(1), entrez-phrase-search(1), epost(1), eproxy(1), esearch(1), espell(1), esummary(1), ftp-cp(1), ftp-ls(1), nquire(1), transmute(1), xtract(1).

go read the whole friend group, fr fr 🫶

and that's the whole page!! this manual came from NCBI, and the date on it is 2021-03-07. vintage but iconic 👑✨💜