Zotero best practices

thanks you very much, that is going to save a lot of trouble . altho I still think maybe I still need some other method too. As I want to bring EVERYTHING under one system in multiple HDDs. I think stuff like Movie collection should go another way but I can save multimedia documents in my zotero. I wish there was a multi vault option for zotero like how it is for obsidian

There is a way to do it: kb:multiple profiles [Zotero Documentation]

Personally, I don’t know that Zotero is the best way to organize such files. Remember, Zotero is first and foremost a reference manager with different goals than file management.

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thanks , i know that but i am looking for a way to manage my files for a while now and I can’t find anything free and reliable remotely as good as zotero. do you know anything to complement zotero?
p.s. for movies I actually thinking about using obsidian and everything (search app) to do that

I don’t, sadly! Might be worth starting a separate thread or asking in the Discord server!

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@argentum, is it possible to replace the color´s name for the category that color represents? For instance, if all my blue highlights are concept definitions, I´d like to have “(concept)” showing up in the beginning of the quote, instead of “(Blue)”. I´ve tried changing extensions.zotfile.pdfExtraction.colorCategories, but the (Blue) label keeps showing up instead of (Concept).

That’s done in the field extensions.zotfile.pdfExtraction.formatAnnotationHighlight, which defines how Zotfile outputs highlighted text when extracting highlights. In particular, you need to use the %(color_category) variable wherever you want your category name to show up. There’s some good examples in this workflow. As another example, I’ve set up the Admonitions plugin with custom admonitions for different highlight types, and then use this in the formatAnnotationHighlight field to produce admonition blocks matching what I’ve set up in the plugin:
<p>```ad-%(color_category)<br />title:&nbsp;<br />%(content) (%(cite))<br />```</p>


Thank you very much for this great summary. Can you please elaborate more on bullet point 7. You are mentioning the “inbuilt printer of obsidian” but I haven’t found this feature yet. So far I use Marked2 with pandoc as pre-processor.


Is there a way to cretae a “Quick Copy” format in Zotero to export (in Obsidian, of course) both reference and item link? The result should look like that:

[Badiou, Alain. *Ethik: Versuch über das Bewusstsein des Bösen*. Translated by Jürgen Brankel. Wien Berlin: Verlag Turia + Kant, 2015.](zotero://select/library/items/INX5ZN8A)

In this way, you have a clickable reference, which would be for my purposes simply AMAZING.


Hey all,
I was wondering if there is a way to skip the need to save the annotations to a dedicated file.
In my usual process I highlight/comment the PDF, then extract annotations, then export the same annotations to a .md file which I then have to open in order to copy and paste its contents to Obsidian (and then I have to manually delete the file).
If there was a way to send the annotations to the clipboard, this would save me a lot of time, given that this process is repeated for dozens of reference notes.
Maybe there’s a setting I’m not aware of somewhere…?
Thanks :slight_smile:

@Sans why wouldn’t you save the file directly to your vault? Maybe I’m missing a bit of context

You could also save the .md file directly in a folder in your vault (this is what I do)

@y.h I didn’t think about it. This is possibly the solution I was looking for!

@argentum I am just stupid :stuck_out_tongue:

In case anyone was looking for an (author, date) version of the plugin:

	"label":"Markdown Item URI",
	function doExport() {
		var item;
		while(item = Zotero.nextItem()) {
			var date = Zotero.Utilities.strToDate(item.date).year;

			var year = date && !isNaN(date) ? " " + date : (typeof item.date == 'undefined'?  "" : " " + item.date);
			var library_id = item.libraryID ? item.libraryID : "";
			var author_lastname = getValidAuthor(item);
			var title = item.title ? "*" + item.title + "*" : "";
			var key = item.key;

	function getValidAuthor(item){
		if(item.creators && item.creators[0] && item.creators[0].lastName){
			return item.creators[0].lastName + "";
			return "";

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Hi @argentum , this figure is exactly what I want! Particularly, I’m interested in the block IDs, I mean adams1979-78f7565. Do they come from zotfile/mdnotes? Are they fixed after each extraction from pdf to md files? Could you point me to a reference where I find instructions on setting up zotfile for these IDs?

As @argentum commented on discord, this is a feature of mdnotes and it’s described at https://argentinaos.com/zotero-mdnotes/docs/next/advanced/hidden-prefs:

  • Setting extensions.mdnotes.obsidian.blocks to true will append a block ID to all non-header text blocks of exported Zotero notes, i.e. to each highlight and annotation extracted by Zotfile.

In the latest beta version of Zotero and the new pdf-reader, you can export the annotations as md-files with working zotero-links. Just a head-up.

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@Kullenej Great news! Thanks for letting us know. The function is excellent and works well – it’s a little tucked away but in the expected place. [Select Annotation ] > Right Click> Export Item >Select Markdown option.

Hi @Marc-A, could you tell me which version of zotero you use?

I just re-installed the latest zotero beta (5.0.97-beta.57+07df7d0de for Linux64) from dev builds. When I right-click on an annotation, unfortunately, it doesn’t display a markdown option. :frowning_face:

@janisc Using 5.0.97-beta58 on macOS. It looks like the function you’re missing was only added a few days ago. I’m sure it will be there in one of the next Linux updates.

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Just in case someone has missed it:
With the new “Markdown export of notes” functionality of Zotero beta-pdf reader, it is not necessary to import your notes through an MD-file… You can also drag-and-drop them into a note in Obsidian (pressing Shift key during drag-and-drop will keep links back to Zotero items and individual annotations).