Zotero best practices

Hey Researchers, What is the process of citing a work and referencing to it in Zotero? I know Obsidian doesn’t have this functionality yet, but is there a standard best practice for citations? Feel free to use Zettlr or whatever as an example.

EDIT by @Whitenoise: @argentum describes her workflow and her zotero extention that pulls annotation and metadata from zotero in this post: https://forum.obsidian.md/t/zotero-best-practices/164/57?u=whitenoise


Adding @WhiteNoise and @Bourdieu and @drsn for your wisdoms


I use Paperpile, not Zotero, but I’m not sure I understand the question. Are you wanting to link to the PDF file in the reference manager, or are you wanting to produce a document that will have a formatted bibliography (i.e. link to the original cited work in a way that can be used for journal submission)? For the former, Paperpile can give you a URL for each item, can Zotero do something similar? For the latter, Paperpile is not currently so good as it is optimized for Google Chrome, but they will have document scanning for plain text eventually. Till then I generate a “citation key” that I can then use for searching when I ready to work on my final document.


Dear Nickmilo

My planing workflow is collecting PDFs on zotero, annotate them on default pdf reader. After reading finished, extract annotations from pdfs by the help of zotfile in Zotero. And use this annotations to write new article. It should be ideal to copy this excerpts ( with linked to pdf in zotero) paste to obsidian and make new notes for each pdf or may be for each annotations. Then while writing use this notes to develop ideas. And if it is possible with new obsdian version, insert reference through ( bibtext addon of zotero) .bib file into obsidian. At the end stage manuscript, styling reference depending on journal with .css styling styles. After all, print as pdf or word files.

Best part of creating this annotation as a note is, you can easliy convert to them permenant or zettel notes ( my suggestion even this notes can be different color to recognize easily ). After 2 or 3 year later you will have a great library to write. By this way you learn more from your read past article also you dont need to read the same article again and again.

Zotero is best for our purpose because it open source, free, annotations have links ( which is very important feature, because after 2 year you want to read this article pdfs so by clicking the link in your permenant note and open the pdf) and betterbibtex addons which is ideal for reference insertion to the markdown files.

To be honest, Zettlr have similar features but dont have graph view. And I think obsidian note system is much better. I hope it will become more excellent with plugins.

I dont know may be my workflow is not so good but may be we can learn more if other users also share their workflows. I hope Obsidian become better than other markdown wiriting tools.

I also suggested Anki plugin especially to memorize some notes easly.


Some links may be helpful

1- https://ikashnitsky.github.io/2019/zotero/
2- https://an-ancient-academic.com/2019/05/22/using-zotero-zotfile-and-scrivener-to-carry-out-research-annotate-pdfs-and-extract-the-annotations-as-notes/


@Luhmann I’m not sure I completely understand my question either! Both your response and @drsn have been helpful to bring light to why and how one might approach citations. Those links are helpful resources as well.

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Thank you for raising this topic of discussion!

I am a PhD research candidate in the area of the humanities, so this might be different than research for STEM-related disciplines.

  1. I look for all of my bibliographic sources online, primarily from my library site.
  2. I use the Chrome Zotero extension to import what is on my browser into Zotero. This step is critical for me, which is why I use Zotero over the other citation applications out there.
  3. I do most of my writing in Word, where I have a Zotero plugin to add my citations. Adding my citation requires me to move my mouse, which is annoying–the [[]] command in Obsidian would be superior to what is available in Word+Zotero. Also the UI from Word+Zotero is serviceable for simple notes (of a few sources and little commentary); but for more complex notes (of many sources and/or expansive commentary), the UI is very frustrating.
  4. I used to manage my bibliographic sources via folders in Zotero, but I’ve become a bit undisciplined. Part of it is because my research requires me to be interdisciplinary so a lot of my sources cannot be easily categorized and part of it is because the UI from Zotero makes organizing all of this a bit clunky.

So for Obsidian to implement a feature like this, using a markdown would make the process superior, even if it’s [[]]. Secondly, being able to import sources that are from the web is probably the best way (e.g., library websites, academic publishing/journal sites, etc.). Lastly, Zotero is nice because you can store and edit various formatting guidelines/styles (I don’t remember how this feature in Zotero compares to other applications). This is imperative since each publisher seems to have its own citation preferences. Yes, Chicago, etc. can take care of most cases, but those who are into publishing need more flexibility/options. This would include endnote and footnote options, etc.

Let me know if you have any questions or if you want to see screenshots, etc.


Thank you for sharing your experience. Would you mind sharing screenshots showing how you add a citation? I’m curious about:

  • how you interact with zotero
  • what the citation looks like
  • what functionality the citation has, ie is it hyperlinked, what does the outputted product look like?

Hey @nickmilo,

interestingly, I plan on using the exact same approach as @drsn, which I thought was sort of ‘hacked together’, but now I am pleasantly surprised that it seems viable. I took inspiration from Zettlr for using Zotero and betterbibtex and from youtuber Shu Omi actually, who suggested using Zotfile for annotation extraction.

Therefore I can second that it would be extremely useful, if Obsidian could help with inserting references in the same way as Zettlr does. However, the beauty of Markdown is that I could use Obsidian for associating knowledge, while using Zettlr for inserting references and publishing to PDF or the like.

One tip I can add is: When copy-pasting the annotations from Zotfile directly to Obsidian, the hyperlinks to the associated PDF is not copied, however when copy-pasting to Zettlr, the hyperlinks are being preserved, wherafter I can go on using these files - including hyperlink - with Obsidian.

All the best!

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1.First annote pdf and extract with zotfille

  1. Extract annotations

  2. Transport annoted notes to obsidian (i make it by drag drop annotations to obsidian and i formated manually )

4.For example: Click second annotation links

  1. it opens pdf page directly

For referecence of this pdf

  1. To site this article while writing cite like that with Betterbibtex addon

  2. After finishing your writen article, refrence will apper in the pdf or word with the help of inbuilt printer of obsidian or pandoc with desired stylign style of journal.

  1. Desired journal style can be found here

Hi all, this is a great thread.

I am not a professional researcher. Though I would like to cite my references more professionally going forward even if all I do is write frivolous blogposts.

I like the idea of correctly citing sources hence I installed Zotero. But as a beginner I find it a bit hard to use.

For e.g. today I am reading https://slatestarcodex.com/2020/06/01/book-review-origin-of-consciousness-in-the-breakdown-of-the-bicameral-mind/

I use zotero and it saves a snapshot into my zotero library. Then I get this in the Zotero library


How do I cite this?

Is it possible to cite a particular paragraph?

And I think the author is a bit problematic. I hope to correct it but not every time i cite slatestarcodex. Is there a way to fix this once and for all?

Sorry if I ask a whole bunch of little questions all at once

Another more general question I have

Most of my sources are:

  1. webpages I read
  2. PDF/white papers I download or someone emailed to me
  3. kindle ebooks or epubs
  4. hardcopy books

I will try out @drsn workflow for 2.

Does anybody have advice for the other 3 sources?


I just installed zotfile. And I wanted to add this pdf which I downloaded to local harddisk.


SO i downloaded it and then I tried zotero desktop app > Add > Link to file

Is that the right flow for this type of PDF? By the way, I haven’t annotated anything. What tools do you recommend for annotating PDF on desktop?

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After I added to Zotero library, how do I link it conveniently in obsidian?

The PDF file itself is located in the same vault but different subfolder as the markdown note I want to put a [[link to the pdf]]


Sorry about making another forum post. Because I am new, the forum does not allow me to put more than 1 image per post

Sorry that was our oversight, bumped to 5 images. Don’t anticipate any spammer or people who want to use our forum as Imgur any time soon! :laughing:


Thank you, Erica

I think 3 is enough. Not gonna complain about 5 tho :slight_smile:

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There is a Plugin for Zotero which makes zitations and bibliography management in markdown files possible:


It saves the citatons in a scannable way so that the markdown doc later can be converted into a .odt or .docx file with any citation style.

If there is interest in a quick tutorial let me know.





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I use rmarkdown which has native citation support (I think part of pandoc)


I save my citations to Zotero then export to bibtex

Each citation entry has a name like @titletext1_titletex2_author1_author2_year

I can then directly reference citations in the markdown by referring to the @bibtex_id


:raised_hand: Thanks

Hello guys,

I hope we can get a tutorial from @Philipp meanwhile I modified a script for Scrivener by a lady called Emilie and here’s the result. It is slow but it’s better than copying and pasting for Zotero. I hope Obsidian has Zettlr-like blazing fast citation insertion soon, meanwhile you can try this quick and dirty solution here: https://github.com/AlexanderSavenkov/Zotero-Obdisian-Picker-Windows


Cool! The overall idea is the same like my workflow I think with the odf-scan plugin.
I will take a closer look this evening.