EDAMNAME(1e)

📦 version 6.6.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

🦋 EDAMNAME(1e) — like, the manual page, but make it make sense 💅

okay so bestie, welcome to EDAMNAME(1e), straight out of the EMBOSS Manual for Debian. grab a strawberry 🍓 and let's get into it.

✨ NAME ✨

edamname — find EDAM ontology terms by name 🔍

it does exactly what it says on the tin. you give it a name, it goes and finds you the terms. main character behaviour, honestly.

🌸 SYNOPSIS 🌸

edamname -query string [-namespace list] -subclasses boolean
         -obsolete boolean -edamname outobo

edamname -help

so basically you have to give it a -query, and you have to give it an -edamname output file. the middle bits in brackets and the booleans are the vibe-your-own-adventure part 🎀

🧚 DESCRIPTION 🧚

edamname is a command line program from EMBOSS — and if you don't know what that is, it's "the European Molecular Biology Open Software Suite" 💖. it's a real one, fr fr.

it lives in the command group "Ontology:EDAM,Data retrieval:Ontology data". yes that's a mouthful, no we don't make the rules.

👑 OPTIONS 👑

💖 Input section

  • -query string — the string you're hunting for. your search term, your one true love, your grep but make it ontology.

🌈 Additional section

  • -namespace list — by default, all the terms come back, no filter, we're collecting them all like Pokémon. but if you want, you can limit the search to one namespace, or a few namespaces. just pass a list. Default value: *

🎀 Advanced section

  • -subclasses boolean — turn this on and the query matches get extended to also include every term that's a specialisation (EDAM sub-classes) of whatever type got matched. it's giving "and her friends too". Default value: N
  • -obsolete boolean — okay so the default behaviour is to not use or return obsolete terms. this option, if you set it, will include all the terms, obsolete ones and all. Default value: N
⚠️ lowkey pay attention to that one — if you flip -obsolete you're pulling in the dusty old terms too, and that's on you bestie.

💜 Output section

  • -edamname outobo — where the results go. it wants a file name for the outobo output. periodt.

💀 BUGS 💀

found a bug? iconic of you. go report it — not me gatekeeping this info:

they do want to hear about it, that's literally what this section is for 🙈

🫶 SEE ALSO 🫶

edamname is fully documented via the tfm(1) system. so if you want the deep lore, that's where it's at. iykyk ⭐

🧚 AUTHOR 🧚

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

  • they wrote the script used to autogenerate this manual page. respect to the automation, honestly 👑

this manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. it can be redistributed under the same terms as EMBOSS itself.

so like, share it, remix it, just keep the same terms. slay. 🌈

okay that's the whole page bestie, and for the cute sign-off: this whole thing is EMBOSS 6.4.0, dated 05/11/2012, and yes the page is literally called EDAMNAME(1e). go find some terms, you absolute legend. 🦋✨

📦 where this page comes from