Zotero 101 - Obsidian Community talks

I’d personally prefer some extra focus on mdnotes, as it’s the only piece I haven’t put into the puzzle yet :yum:

I’m only a hobbyist in this realm, and very new to Zotero. In fact I started using it after discovering Obsidian. My problem - The majority of Zotero tutorials focus heavily on very specific uses - mostly academic.

Although I’ve really only been saving web content (almost purely as .pdf’s), I do plan on building a Goodreads-style media shelf to track things I’ve consumed, or want to consume someday. This would include ALL media - books (fiction and nonfiction), music, film, television, et cetera.
Zotero is pretty straightforward for research. It would be neat to see if others have thoughts on how those more …casual… things could be organized, annotated, and eventually extracted once finished.

That, and since I’ve abandoned folders for most purposes, Zotero Collections scare me just a little bit :slight_smile:

I have managed to cobble together Zotfile and Mdnotes into what I feel is a pretty usable output, so I’m not quite as interested in that. However, it took me no end of fiddling and trial-and-error to get there, so I certainly understand this talk could be Mdnotes heavy, and with good reason. I suspect that will be on the minds of most that participate. :wink:

I guess the bottom line is I (personally) would look forward to the Zotero/Obsidian specific content as much or more than the extraction tools. Basically, it would just be cool to see how other real people have used Zotero.

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The thing I’m most stuck on is changing the output format from the default. From the documentation it looks really technical and I’m a little scared of it.

Thank you for doing this!
Will this be recorded?

@Kullenej I’m not sure yet! I’ll announce it next week if it will!

Please record it if it’s possible. There already is an Obsidian talk channel in Youtube.

(I won’t be able to attend it sadly - I am helping a friend out on that day)

I’m aware of the channel! I still haven’t decided if I want to record the session or not, but in case I don’t, and you can’t make it to the meeting, do not despair! Cat’s wonderful write-up already covers a lot of what I’ll be showing and some more advanced topics (e.g. dataview): Zotero -> zotfile -> mdnotes -> obsidian -> dataview Workflow. Bri’s talk in the Obsidian Office Hours channel could also be of interest to you: Merging library & information science and PKM - How Bri Watson uses Obsidian - YouTube

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I have a lot of technical (non-academic) PDFs stored locally on my laptop that I want to annotate and move into zotero. Does the workflow differ from PDFs downloaded from the web. When I initially setup Zotero and dragged in a local PDF, I got an error when I tried to extract the annotations with mdnotes. It said that I needed a parent item so I used the create parent item and entered the authors name manually. Once I did that, it was happy and did the md conversion. Can you discuss what else would be considered best practice in respect to manually populating the metadata. Additionally, recommended folder structure in Zotero libary. Thanks!

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Zotero can extract the metadata of PDFs that have the information properly input and create a parent-item from that. To enable this, go to zotero’s preferences, and in the “General” tab, enable “Automatically retrieve metadata for PDFs”.

For folder structure, you can use zotfile’s wildcards to get it to automatically move your files into particular folders using the wildcards listed here, meaning you can organise your library however you best recall files, whether by collection, year, author’s name, item type, etc. It’s advisable to find what works best for you, rather than go with what others recommewd here. For instance, I recall subjects best, so I have zotero collections organised by subjects, and zotfile automatically moves PDFs into the relevant folders labelled according to the collection (wild card %c). Many people prefer organising by author’s name instead, as that’s how they recall files best - by who wrote it - and therefore can find the article if the PDFs are organised by author’s name.


Edit: I believe I now know, it is the Obsidian Community Talks channel on YouTube. Will be there! Thanks for setting these up!

Hi @miguelmarcos, the talk will be held in Zoom! The announcement (and reminders) for the talks usually happens on Discord (click on the arrow thingy):

The specific message with the announcement is here: Discord

Hope to see you there tomorrow!

Oh, OK. Thanks for the heads up.

Here are the answers to the remaining Q&As from today’s session


This is a great question:

Imagine we are writing a paper and we use citekeys in the [citekey] format for pandoc to render it properly as a citation. but we also have md pages in our vaults which can be found at [[citekey]]

How would I link the md page without having to write these twice when referencing the source in the paper md draft: “extract from paper - [citekey] [[citekey]]”

I’m a bit opinionated on this, my notes use [[citekey]] , and is what I use in obsidian… I don’t use [@citekey] very often because I do my writing in LaTeX, but when I do use them it’s as part of the final product (that I’m exporting to PDF). So far I do it when I bring my paper back from LaTeX → markdown to store in obsidian

When annotations are converted to markdown, is it ok to rename the md file before moving it to Obsidian?

Renaming the file when you create it should be alright! If you rename it afterwards, you might need to update the links added in Zotero by mdnotes

Sometimes when I use Citation plugin Word, usually adds the first & last mame of the author, e.g APA. I just want to automatically display only the last name.

You might need to use a different citation style that uses the authors last names

Do you know any way to get highlights from Calibre/Epubs?

I don’t, there might be a plugin for it that I’m not aware of: plugins [Zotero Documentation]

What is the timeline of this Zotero support/change? Coming soon?

If it’s referring to mdnotes, coming as soon as I have some time! Hard to estimate a timeline

I’m trying to use custom placeholders, which I set in the config editor. They are not being rendered when choosing 'Create full export note". Do you know why?

Probably you are adding the placeholders to the wrong template, the placeholders should be in the Mdnotes Default Template.md file (you’re using single file exports)

what OS are you using? Your screen looks rad!

Thank you! I’m using Ubuntu with i3 https://i3wm.org/

I have Zotero loaded and up, but it looks nothing like what you are working in. What is the tool she is showing us? Vault? Word processor? ???

This is due to my system setup, I’ve added this theme and that changes the Zotero appearance: https://github.com/EliverLara/Nordic (I use a nord color scheme almost everywhere)

how do i get memos to obsidian?

If those are the little yellow notes, then using the Export to markdown menu should do it

My main question is “how do I change how the formatting looks when it gets extracted and plopped into Obsidian” for what it’s worth.

I hope the tag example helped, but if it didn’t let me know, and I can set up a couple of gists with more examples for customizing the formatting


Alright! Videos and handouts are up, and I’ve just added them to the bottom of the main post:

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I have Zotero loaded and up, but it looks nothing like what you are working in. What is the tool she is showing us? Vault? Word processor? ???

Apparently there are technical reasons well beyond my understanding that limit the Zotero developers’ ability to create a Dark Mode option. Other folkx (also with technical capabilities well beyond mine) created a CSS file to simulate a dark mode. For Windows it is available here; for Mac here. NOTE: The location for Mac is a little tricky: Create a Chrome folder inside /Users/username/Library/Application Support/Zotero/Profiles/bunchofletters.default (mine is named “lio0a6gq.default”) and copy the userChrome.css to that folder.

Thanks for the video! I was surprised that the obsidian citations plugin wasn’t even mentioned. I assume that this is because @argentum isn’t using it? In any case, I’m trying to wrap my head around how mdnotes and citations relate to each other.

There is obviously some overlap in the functionality: both can create notes with metadata for articles/books in zotero. One pushes them from zotero to obsidian, the other pulls them out of zotero to obsidian. Both allow me to customize the templates based on which those notes are created, so I assume, I can create more or less identical notes in both. But I like the way how citations allows me to create a reference to a book/article for which I don’t even have a literature note yet (it creates a link to a non-existing note). I also like the way how I can create a literature note in obsidian and pull over the metadata from zotero.

So what I’m wondering is: does it make sense to use both the citations plugin and the mdnotes add-on? If so, what is a good way of setting this up?

At the moment, I’m thinking to create the meta-data notes with the citations plugin and push my annotations notes from zotero and transclude them in the meta-data note. But I still need to figure out how I need to name my notes-files so that this can be automated via a template. I’m also not sure what mdnotes features I’m missing if I go down that path…

Thanks in advance for any clarifications.

@tophee we do cover it (albeit very very briefly) in the 2nd part when I talk about Better Bibtex. The talk itself was more about how to set up Zotero and its plugins (but it is roughly what I covered for the citations plugin too).

There is some overlap between Mdnotes and the citations plugins, it depends on the information you might want to include in your templates which one might be more suitable.
The citations plugin has access to what is exported in your bib/csl file. Mdnotes has access to any Zotero field and meta information (e.g. collection names, dates, etc.) or the ability to add/format your extracted annotations and fields, e.g. what Cat demoed here and/or adding block IDs to your extracted annotations.

You can still use both, depending on your preferences. Personally, I find the citations plugin great for navigating my literature notes in Obsidian! But as you said, you can use it to create templates too and export annotations with mdnotes or just the citations plugin too!


You are right, of course. It is right here:

That seems like a humble way of saying that Mdnotes is better because it has access to everything in the zotero database :wink: But I do agree that using the citations plugin still has its place for quickly referring to books and articles that are in zotero (and which you may not even have read yet).

So I think for it to work well with mdnotes, I should make sure that it produces notes whose file names are identical with the metadata notes created by mdnotes, right? - It obviously depends on what exactly you want to achieve, but I agree with your approach of keeping your own notes (in obsidian) separate from the literature metadata and annotations so as to be able to update those without losing your notes (in obsidian). So let’s stick with that approach for now.

As I think about it, I actually see two ways of integrating citations and mdnotes.

  1. One is the one that came to mind first (above): use the same file name for the metadata-note in both citations and mdnotes. You can refer to that file even when it doesn’t exist yet or you can let citations create a preliminary version which will be overwritten once you export annotations via mdnotes.

  ┌─────────┐       ┌───────┐
  │citations│       │mdnotes│
  └────┬────┘       └─┬─────┘
       │              │
     writes      (over)writes
       │              │
     │ main note-file  (incl. metadata) │
     links to
       │  ┌───-─────────────┐
       ├──►annotations file1│
       │  └───-─────────────┘
       │  ┌──────-──────────┐
       └──►annotations file2│
  1. The second one is perhaps better, but adds some complexity. Instead of letting both plugins write the same main-note-file, which then links to the annotation files, we could add another level in the note hierarchy: citations would then create the main-note file which links to the mdnotes metadata file as well as all the annotation files. Only mdnotes overwrites these. And thanks to your ingenious idea to create the block reference id by hashing the annotation, all links and transclusions will still work after mdnotes updates the annotations (as long as annotations are not changes but only added).

    ┌─────────┐   ┌────┐   ┌─────────┐
    │citations│   │user│   │ mdnotes │
    └────┬────┘   └─┬──┘   └─┬─────┬─┘
         │          │        │     │
       creates    edits    writes writes
         │          │        │     │ 
       ┌─▼──────────▼─────┐  │     │
       │ main note-file   │  │     │
       └─┬────────────────┘  │     │
         │                   │     │
   links to/transcludes      │     │
         │                   │     │
         │      ┌────────────▼───┐ │
         ├──────► metadata file  │ │
         │      └────────────────┘ │
         │                         │
         │      ┌──────────────────▼─┐
         └──────► annotation files   │

In fact, with that (second) approach you don’t even have to split the metadata and annotation files and just write them into a single file, depending on preference.

What I like about approach 2 is that it has a dedicated space for my own post-reading reflections in the main note-file. Integrating the annotations i make in the pdf during reading with more elaborate reflections in obsidian after (and sometimes already during) reading has been a major headache for me. It looks like this could be a solution.

Does this make any sense? (I haven’t tried it in practice yet…)

BTW: the diagrams show the files for a single article/book in zotero.

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Not necessarily better, just different! If you don’t need access to those things, the citations plugin might be better, since it’s easier to set up if you’re not very technical, and you can trigger everything from within Obsidian without needing to configure (the sometimes extremely confusing and unfriendly) Zotero settings.

It does, I think! That’s roughly what I would’ve suggested: You can create your “main” note with the citations plugin and export your annotations using the Export to markdown menu in the little yellow Zotero notes. If you use multiple files like I do, in mdnotes, you can automatically transclude/link the annotations into your main note. I think people have managed to set up templates with the citations plugin to do this as well, but I’m not familiar with how! However, if you are using a single note with everything (metadata, annotations, etc), the citations plugin is also able to include everything in your note (I don’t know how to do that however).

In the end, as with all these things, it’s mostly a matter of preferences and of willingness/ability to invest some effort in the configuration.