Zotero best practices

@Ditto these two settings are a bit confusing (I always manage it after a bit of trial and error). Maybe the community talk portion dealing with Zotfile helps a bit? https://youtu.be/LaEt9cqkj3I

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it looks very interesting. do you having more detailed info on what it is? (i couldn’t find any on the website)

for me having may bookmarks in browser, my books in zotero and my notes in obsidian is annoying, not mentioning other files that i keep in folders

i messed with it some weeks ago and it is not changeable. I wanted to add new categories to it (as it doesn’t cover all the colors adobe reader supports) and I couldn’t change them at all. Documentation on it is poor

It’s not changeable on the title (from what I recall), but it should work on your note content.

yes that is doable, but the setting for that didn’t make sense to me. I can recall from top of my head now but I remember there was some weird problems

Id be really interested. My main workflow involves PDF/Webpages → Zotero organiization + hypothes.is annotation → Obsidian → Anki.

I love obsidian for the connectivity and visualization.
Its really clunky. Can protolyst do all this?

I’m searching for a way to generate a modified file link based on the one that’s automatically created at the end of each Zotfile extracted annotation. This link, however, would replace the current link to the pdf or annotation with a more general link to the reference, as such. In other words, is there a way on either the Zotero or Obsidian side to generate such a link?

Currently, I copy and paste into Obsidian note the extracted annotation via the following link:
([Schulman 2016:12](zotero://open-pdf/library/items/NKJNCHWB?page=12))
Preview mode result:
(Schulman 2016:12)

What I’m trying to do is generate a zotero link that I can copy paste into zotero like this:
([Schulman 2016](zotero://select/library/items/))
Preview: (Schulman 2016)

Using Zutilo use the “copy select item links” command and it generates part of the link to I’m looking for:

Unfortunately, I’m too inexperienced to know how to use Obsidian (or Zotero) to automatically generate a reference link in Obsidian, e.g., (Schulman 2016)

Thanks in advance for any help you might be able to offer. I’m so grateful for all your work and the collaborative spirit of this forum.

You could try @silent 's plugin here: Zotero best practices - #72 by silent

Consider using the Citations plugin as well.

I think indeed the Zotero translator by @silent does this. I can’t remember if the readme on his repo explains how to install it, but I imagine it does.

I’ll also paste this handy tip from the Discord server (credit to @WhiteNoise ):

you can even put this [Open in Zotero](zotero://select/items/@{{citekey}}) in the template to get a direct link to the item in zotero automatically


Zotero translator by @silent does the trick. Thanks to @allanelder and @argentum for quick reply.

Re workflow: my thought is that Obsidian Citations plugin is perfect for writing projects that ultimately require properly formatted of citations but–as people seem to appreciate in the case of Zotfile’s extract annotations–the kind of link generated by @silent Zotero translator can be particularly useful when reading and taking/making notes.

If I had posted my question here earlier I might have saved three days of failed efforts to reinvent the wheel. :blush:

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Have you guys tried adding multimedia files to Zotero? I think Zotero is an excellent app for reference management but I worried that I can’t have all my files on a central location /HDD. IS there a way to do this. for example telling Zotero to store big files on an external HDD and just keeping a parent item to keep metadata.

@Archie Zotfile should take care of that! The community talk should give you an idea of how to set it up: https://www.youtube.com/watch?v=LaEt9cqkj3I. There is also more info here:

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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!


@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.