Obsidian and Zotero: Possible future integration?

edited June 15, 2020
Within the Zettelkasten community, a new text editor is quickly becoming popular. The developers are astonishingly productive, so it already seems remarkably polished and has a sizable and fast-growing user base. (I recently learned that it's led by the pair who make Dynalist, if anybody's familiar with that.)


It's hard to explain why Obsidian is so exciting without understanding Zettelkasten. It's a fascinating, weird, and – in my opinion – very promising system of taking and organizing notes. Here's the best primer I've seen:


You don't have to use the Zettelkasten system to use Obsidian, but that's what it's designed for. Probably won't be all that exciting if you don't use it.

Anyway, I wanted to put this on your radar because over in their forums, one of their most visible team members enthusiastically indicated that they'd be interested in Zotero integration.


My hope is that somebody from Zotero might reach out just to establish an open communication channel.

Why am I bringing all this up now? I remember a conversation about why Scrivener is unlikely to ever have Zotero integration. The gist of it, if I remember correctly, is that Scrivener made some decisions during it's early days that would essentially require either Zotero or Scrivener to rewrite tons of code from scratch. It's simply too much to ask of either project. Because Obsidian is still so new, that situation can still be avoided – perhaps with nothing more than an exchange of few emails. "If you avoid X and do Y, then full Zotero integration will be possible" could go a long way.

For right now, I think just writing an email that says something like "Hello, we're happy to hear you're interested in Zotero integration, just want to let you know that we're receptive to that possibility, let us know when/if you want to talk" would be sufficient. The idea is simply to open the communication channel.

I have no affiliation with Obsidian. I'm just a happy user of it and Zotero who remembers an old conversation about Scrivener and sees an opportunity to head off a repeat of that situation. Even if you don't reach out like I hope you will, maybe some good can come simply from putting it on your radar. :)
  • As a markdown editor (as I understand it), Obsidian would indeed best be served by similar integration as Zettlr. Zotero already provides the requisite infrastructure, someone just needs to hook this into Obsidian. All the relevant tools (BBT, pandoc) are already listed on that thread.
  • Thank you for that link to the Zettelkasten primer — I was aware of the method but that's a wonderful explanation.
  • edited June 16, 2020

    Yeah, it's very similar to Zettlr, but a bit more ambitious or a bit less minimalist (depending on how you look at it).

    Zettlr already has a lot of Zettelkasten-focused features that make it quite different from most markdown editors. It has features like linking between files and a navigation sidebar designed for quickly searching non-hierarchical filing systems. It's awesome.

    Obsidian is Zettelkasten-focused like that, but has even more features. For example, it automatically detects backlinks and has a built in graph to show the web of connections between Zettels (notes). These are awesome features. It still looks pretty minimalist overall, but the additional functionality is actually pretty astounding. I think that's why it's becoming so popular so quickly.

    By comparison, all the regular markdown editors I've played with over the years – iA Writer, Typora, Dillinger, and others – are beautifully stripped down notepads that only have syntax highlighting and/or live export previews. Maybe they have grammar checking, maybe they have a "focus mode," or maybe they have other features besides different UIs to distinguish them from each other. But still, they're all basically minimalist notepads. (This isn't criticism at all. It's exactly what they're trying to be, and they'd be worse at achieving their goals if they took it further. The three that I linked to are as functional as they are beautiful. A lot of thought has clearly been put into them.)

    Anyway, Obsidian is on your radar now, so I've at least achieved my minimum goal. I'm content with that. :)


    You're very welcome! I spent a couple hours trying to find the best introduction to Zettelkasten, and that's what I settled on.

    If you're curious enough that you want to get started, I recommend reading How to Take Smart Notes by Sönke Ahrens and trying to take notes as you go. It feels a bit like a chicken-and-egg problem at first, but it works. In fact, I wonder if Ahrens planned for people to do exactly that when he was writing the book.

    And if you have questions, I've found /r/Zettelkasten to be super friendly. I think the entire community remembers what it was like to try wrapping their minds around Zettelkasten for the first time, so they're especially welcoming and receptive to newbie questions. Despite what it may seem, I am still one such newbie. I'm still going to them with basic questions regularly, as do many others.
  • just to clarify: my point was not to say that Obsidian is redundant or the same as Zettlr (I wouldn't be qualified to say anyway), but to point out that it could use the exact same, already existing technology/toolchain to integrate with Zotero
  • Oh no, I didn't get that impression. Don't worry. :)

    Because of your parenthetical note, I wondered if you might not have a lot of experience with markdown editors, so I thought I'd talk briefly about them with links so that you could open them in new tabs to quickly survey the field. The goal was to provide just enough info to give a sense of what they are like in general, and why the Zettelkasten-focused are best regarded like a different species.

    I also figured that even if you were simply being humble about your level of understanding, others – like Mark, possibly – might benefit from my extremely criminally brief comparison of markdown editors.
  • Please do it! Would be great for both Zotero and Obsidian.
  • In terms of getting notes and metadata into Obsidian (as opposed to citing within notes there), you might be interested in my Zotero to Roam exporter: https://github.com/melat0nin/zotero-roam-export

    I'm currently comparing Roam and Obsidian; if the latter seems better I might extend the exporter to cover it (at the moment its JSON format is Roam's but I think it should be relatively simple to change)
  • edited August 12, 2020
    Another possible model is the rbbt Zotero/bibtex to Rmarkdown connector (https://github.com/paleolimbot/rbbt). It seems to offer a few advantages out of the box: (1) RStudio and rbbt are FOSS without the $180/year rental fee, (2) RStudio + R can do lots more (at least 6,000 packages worth) than just prepare markdown notes, (3) Rstudio integrates well with GitHub (https://resources.github.com/whitepapers/github-and-rstudio/), as does Obsidian (for example, https://forum.obsidian.md/t/share-obsidian-notes-with-github-gist/2194), and (4) this would also work with Gitjournal on mobile devices.

    Of course a few issues need to be ironed out: (1) It would be nice to have a note template in RStudio to simplify note taking, (2) notes should be stored in a single common directory (like Luhmann's cabinet) rather than in a RStudio project directory devoted to a specific project, (3) each of the various applications (Obsidian, RStudio/R, Gitjournal, etc.) would necessarily not be able to interpret the other's special code. On this last point, for example, Rmarkdown accepts "chunks" of R code that can be run when the document is compiled. So, for example, it can generate a graph at compile time. Maybe this is a job for an Obsidian plugin that calls R. Then again, most people could probably live without this feature. (A note on someone else's work might insert a graphic, but most such notes won't need to generate the graphic from raw data.)

    And, oh!, with this kind of integration you can do this: https://www.alexchamessian.com/post/visualizing-your-zettelkasten/
  • RStudio has actually just added native Zotero integration to its daily build, so there soon won’t be any need for Zotero plugins at all.
  • I strongly support the call for the possibility of integrating Zotero and Obsidian!

    I switched to Zotero during my master studies as I was unable to productively use all the features of Citavi during my bachelor thesis (instead, I spent more time on organizing quotes and knowledge). The fact that zotero is straightforward and open source, is the main reason for me to recommend zotero to my students. However, both in my current dissertation and teaching, tasks are becoming complex and the integration of Zotero and Obsidian would be highly useful.
  • This is something you would need to ask Obsidian to integrate—Zotero has provided all of the necessary infrastructure for them to do so.
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