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Ric Raftis Consulting

How To Use Zotero With Obsidian For The Best Note-taking Experience

Ric Raftis consulting logo

Introduction

For quite some time now, all attempts at getting Obsidian to talk to Zotero have failed. This has not been with just one plugin, all have been tried, but none worked satisfactorily until now. Inspiration and determination came because of Bryan Jenk’s latest video on the Zotero Obsidian plugin. However, the workflows demonstrated by Bryan and also Danny Hatcher were far in excess of my requirements. The desire was to organise something reasonably basic that could be built on as needs changed or features became visible in both Obsidian and Zotero and the workflow.

As a result, this article and video will step through the process of getting Obsidian up and working with Zotero at a basic level on which you can build over time.

Zotero

Zotero is a reference and research assistant that is both free and exceptionally powerful. Other programs do exist such as MyBib and Endnote, but none except Zotero can interact with Obsidian to my knowledge. Not only does Zotero offer the ability to organise your research, but it also provides the ability to annotate PDF documents, which can be extremely handy. Furthermore, it will generate citations and bibliographies in a large number of academic formats and scrapes considerable information from the sites you visit and bookmark. There is also a browser plugin so you can add papers direct from Chrome, Firefox and Safari. The first step in this process will be to download Zotero and install it on your computer.

Zotero Plugins

As you will see when you install the Zotero Integration plugin, you need to have a plugin installed in Zotero. This is BetterBibTex that makes it easier to manage your stored data and provides the formatting styles for export to Obsidian. While you are installing Zotero plugins, there are a couple of others that may come in handy. ZoteroPreview provides another tab in the right-hand pane where you can see the format of both the bibliography and inline citation. Another plugin that is very useful is Sci-Hub which can provide access to the full text of many papers. After installing these, you will need to restart Zotero.

Obsidian Zotero

With Zotero installed, go to Obsidian and install the Zotero integration community plugin. Enable it and read the documentation both in Obsidian and also on the plugin page. There is quite a bit to digest and some of the information was found to be somewhat obscure, which had frustrated previous attempts to get this plugin working.

As mentioned earlier, this workflow was only developed in the last day. Consequently, the setup of the plugin is based on defaults and could well be improved over time.

Figure 1: General Settings in Zotero Obsidian Integration

Figure 1: General Settings in Zotero Obsidian Integration
Source: Screenshot created by the author.

In the above image, you can see the first lot of options to be configured. The first one is to set the database to Zotero. Next is the location in your vault where you want imported notes to be stored. If this is left blank, they will be stored in the root directory. If necessary, create a folder to store your notes. The rest of the options have been left at the default.

Figure 2: Zotero Integration citation format screenshot

Figure 2: Zotero Integration citation format screenshot
Source: Screenshot created by the author.

The next options to set up are your citation formats. You add and configure these yourself and name them accordingly. Whatever you name them will display in the command palette when you invoke them unless you assign hotkeys. The first one above has been named “Cite” and will be used for inline citations that are information prominent, such as (Smith & Bloggs 2023). Unfortunately, there is not a pre-written format for author prominent citations e.g. Smith and Bloggs (2023) suggest……. However, you may be able to set that up using a template.

The output format field under the name of the output is a dropdown box where you select the format to be applied. In the image, you will note there are 2 formats with one for citations and the other for bibliographies. Although the plugin allows you to apply a bibliographical format, it is only for a singular reference. It is probably much easier to create a full bibliography in Zotero on completion of your paper and paste it into the article at the end.

The final option to be set here is the citation style. Note the important rider that the style must be installed in Zotero. Many styles are installed by default, but if your institution uses an obscure style, you may find it in the Zotero Styles Repository. Once installed, you set the style in Zotero and also in the Obsidian plugin.

Figure 3: Zotero Integration output format screenshot

Figure 3: Zotero Integration output format screenshot
Source: Screenshot created by the author.

Finally, the setup requires you to complete the import format area. This determines what information comes into Obsidian from Zotero via your template (which we will get to shortly), where the template is stored and where your notes will be stored when you create them.

As you will see in the image, the style has been selected, in this case Melbourne Polytechnic Harvard. For the purpose of output, a folder called Zotero has been created in the vault. So the note will be stored in the Zotero folder with the note name being the title of the article. The default is the citekey, but I prefer my notes to be named by the title. Any images will also be stored in the same folder.

The default pre-pend for image files is “image” but I have changed it to the citekey which has more meaning from a search perspective. The rest of the options can be left as they are.

Zotero Notes Template

Templating is where most people seem to run into trouble. It is understandable that many people struggle to get this integration working because of template syntax. It makes it even more difficult if you are not a programmer. The template being used here has been cobbled together from a few that have been found online and references will appear in the footer. It has been adjusted for my purposes with the colour codes for my highlighting and a few other minor adjustments but it is the collective work as a result of standing on the shoulders of giants. Many thanks to all those who have made their work available online.

Download the template.

It is not the intention of this article and video to overcomplicate things, so here is a link to a template that works and has been modified to suit general use. It is available for a minimum of $2 to make it affordable for anyone who values their time, but if you want to support my work with a bit extra it is much appreciated.

It is worth noting that there is no standard colour coding for highlighting notes so the following has been adopted for use within Zotero and within the template.

Red – Very important, critical
Yellow – Interesting point
Green – Supporting argument/example
Orange – Disagree with author
Grey – Vocabulary, names and dates, definitions
Blue – Related, research this paper

Using these colours when annotating notes in Zotero will ensure they are correctly allocated when you pull them across with the template in Obsidian.

Installing the Template

Once the markdown file has been downloaded, simply move it to the templates folder in your vault. Make sure this is the same folder you have nominated in the Zotero Integration plugin options.

Using the Plugin

The plugin has been set up so you are able to access 3 items at present. These are an inline citation (information prominent), a bibliography or a paper with annotations. You can set up hotkeys for all these can set upfunctions, but this process will step through using the command palette.

Importing Papers

You do not need to start a new note to use this workflow. The new note with the paper included is created with the plugin.

With Zotero open on your desktop, use Ctrl + P for Windows or Cmd + P for Mac to open the command palette. Simply type “zot” into the search bar and the Zotero options will appear. Choose the one for the citation format that you set up. In the example it was Melbourne Polytechnic.

Figure 4: Selecting Zotero’s Paper Import

Figure 4: Selecting Zotero's Paper Import
Source: Screenshot created by the author.

The Zotero search box will pop up. (One word of caution here is that it was found that sometimes it was hidden behind Obsidian. This meant using Alt + Tab to access the window.)

Figure 5: Zotero search bar

Figure 5: Zotero search bar
Source: Screenshot created by the author.

Begin typing in the name of a paper from your Zotero database and it will selectively display papers fitting that criteria.

Figure 6: Zotero search bar showing available options

Figure 6: Zotero search bar showing available options
Source: Screenshot created by the author.

Now select the paper that you are wishing to use and it will bring up the citation for confirmation.

Figure 7: Selecting the paper by citation

Figure 7: Selecting the paper by citation
Source: Screenshot created by the author.

The paper will now be imported into your Obsidian vault and open ready for you to work on.

Figure 8: Extract of imported file showing frontmatter

Figure 8: Extract of imported file showing frontmatter
Source: Screenshot created by the author.

The above image shows a screenshot of the top of the note, including the frontmatter. You may note that YAML is not used in the frontmatter, but that is a personal preference;

Figure 9: Screenshot of Very Important and Critical notes imported

Figure 9: Screenshot of Very Important and Critical notes imported
Source: Screenshot created by the author.

Above in Figure 9 is a screenshot showing the “Very important and critical” notes that were highlighted in the annotated PDF using the colour red. The template displays each highlighted note in a callout with any notes you have made appearing beneath as a bullet point. The template cycles through all the highlighted notes and lists them by colour of highlight.

Other Uses

Zotero and Obsidian have many other uses, not to mention expanding the template to contain more data. It is not desirable, however, to confuse the reader with complicated examples. Suffice to say, the plugin will import inline citations and bibliographies. It is preferable to build your complete bibliography on completion of an article and export it from Zotero which will be covered in a future article and video.

Conclusion

As mentioned in the introduction, it has taken quite some time to get this plugin working but it has certainly been worth it. It is hoped that the explanations here will assist others implement a far more speedy solution. Should you have questions or comments, please feel free to leave them. Also, if you have other uses for the plugin it would be great to hear of them and how you are using them in your workflow. Oh, and here is the link to the template again. Zotero2Obsidian

Bonus Video

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17 thoughts on “How To Use Zotero With Obsidian For The Best Note-taking Experience”

  1. I am having trouble following the workflow between figures 8 and 9. I have successfully imported a document from Zotero. I then marked it up with a red highlight and added a note,
    How does this get transferred into the note

    1. Hi Neil,

      Once you import the note, you have two choices. Either continue your annotation in Zotero itself, or in Obsidian. If you do it in Obisidian and import the Zotero note again, it will overwrite the Obsidian note and you will have lost your changes. My suggestion is to make all your annotations in Zotero, delete the Obisidian note and reimport the Zotero one.There are really several ways of managing this, but ultimately it will be up to the workflow you wish to use. I hope this helps.
      Cheers,

  2. Thanks ever so so much. The video was great

    Very helping insights from you which is accelerating my ability to use both these tools, which I have recently stumbled across

  3. Thank you so much for the video and template. I bought the template and put everything in place, but I’m running into a problem where any new annotations I make in Zotero are not imported into the template. It will work, however, with old annotations on papers that I made in advance of taking the steps outlined in your video. Any ideas why? I followed the steps exactly…

    It will import the new annotations if I use the “Zotero: Import Notes” command in Obisidian, but I just cannot get it into the template. All plugins are updated (better bibTeX in Zotero, Zotero plugin in Obsidian).

    This functionality is exactly what I’ve been looking for, so any ideas would be appreciated.

    Thanks!

    1. Hi Mark,

      I only just saw your reply. I find the best way is to delete (or rename) your original import note and then bring the new one into Obsidian with the revised annotations. This is how I do it so it maintains a readable structure. Let me know how you go.

  4. Hi Ric, thanks for your guidance with this. I installed your most recent notes template with the properties. When I select the file from zotero that I want to import, no new note is created in obsidian. I’m wondering if you can help me figure out what’s going wrong here? thank you.

    1. Hi Jessie,
      That’s a hard one without seeing what’s happening. One thing to check though is that your import format i.e. APA 7 is the same in Obsidian and in the Export preferences in Zotero.

      Cheers,

      Ric

      1. Thanks Ric. I realised I needed to have a “parent” item in Zotero for the annotations to be imported to Obsidian. Do you know if there is a workaround for this? I also noticed that the template doesn’t pull the literature note from Zotero into Obsidian. Is there a different plugin needed to do that? Thanks again and I appreciate your time.

        1. Hi Jessie,

          Not sure about the parent item thing. I can tell you though that the template does not pull the literature note into Obsidian, only the annotations and the notes you have made to them. I am currently working on a course with a different workflow that will allow you to do this though. So, all the annotations will be in Obsidian rather than Zotero.

          Cheers,

  5. Hi Ric, thank you for your guidance! This comment is just to let you know that I’m really glad that you’ve decided to publish this article and the accompanying video – I’ve been struggling to understand the tutorials on the web to get Zotero and Obsidian to link but yours has been fairly easy to get through.

    Your template also works well on my setup 🙂

    Cheers!

  6. Hi Ric,
    Somewhere you posted a tweak to Zotero to get the box where you search for references to always appear on top. After a Zotero update I think I need to redo the tweak but can’t remember how it is done.
    Thanks for your help.

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