From Zotero to Obsidian : a tag based workflow in pictures

edited August 19, 2022
This post has been created in continuation of a couple of templates shared. See this thread for more context.

Workflow description:
1. Use Zotero pdf reader to annotate your readings
- highlight, annotate
- tag your highlights, tag your post-it aka fleeting notes
- make comments
2. export to your obsidian vault
3. use obsidian as you much as you like to refine your knowledge system


I used the following templates to do so.
A. Template for tags and highlights in Zotero:
edit the advanced preference extensions.zotero.annotations.noteTemplates.highlight as followed:
{{if comment}}<p>{{comment}}{{endif}}<blockquote><i>{{highlight}}</i></blockquote>{{citation}}{{if tags}}<br/>#hgh/{{tags : tags join=' #hgh/'}}{{endif}}
- see it at work from Zotero 6.+ reader interface
- see results after export from Obsidian interface

B. Template for tags and post-it notes in Zotero:
edit the advanced preference extensions.zotero.annotations.noteTemplates.note as followed:
<p><i>Note:{{comment}}</i>{{if tags}}<br/>#note/{{tags : tags join=' #note/'}}{{endif}}<br/>{{citation}}</p>
- at work from Zotero
- results from Obsidian

Overall results:
- from Zotero
- from Obsidian: here and here too

Hope it works for you and that the links are correct, let me know if not.
Any feedback is welcome.
It remains more of sketch than a full usecase but I think it gives an idea of what one could do with the reader-anotater features from 6.0.
Also, it emphasizes the nested tag feature on Obsidian side.
  • Hi, This is a tremendously interesting post. I am using Zotero 6.0.13 and am using Zotero's pdf viewer. I believe I am following your suggestions to the letter, but get stuck on step 2. I can annotate the pdf, but do not see any options anywhere that will allow me to export all the annotation notes. I have also tried closing and saving the pdf. When I right-click on the PDF listing in Zotero, there is no option shown to extract the note. What might I be missing?
  • Hi Bloms and many thanks you for your comment,
    you might want to try a right click from the child note itself, not the pdf neither the parent item. Note though, I just checked and I could export notes from right clicking on the parent item.

    For any doubt, it is true that I did not mention I installed Md notes plugin for Zotero, see it on https://github.com/argenos/zotero-mdnotes.

    Also, you could try to drag the note and drop it to your obsidian interface if I am correct.

    Extra note: I am currently considering doing a variation of the above with [[ ]]s instead of #s. That implies moving from tags to links, which is another approach that I did not explore yet. Discussions on the differences between the two are addressed in obsidian forums.
  • Apologis for sidetracking; I'm interested in a similar workflow, but one additional thing I'd like to have available is a way to include context around the highlight saved in the note annotation that can then be exported to Obsidian/MD app.

    For example, maybe a variable like {{paragraph}} that gives the entire paragraph in which the highlight is found or some equivalent that provides ~3 lines above and below / ~10 words before and after the highlight. Perhaps something like what https://github.com/elias-sundqvist/obsidian-annotator offers.

    I would want to use additional context in this and other workflows - does this sound appealing to anyone else, or do you know if there are other discussions on this?
  • edited September 27, 2022
    Thanks for your comment, that looks interesting. My humble guess is that the only way to do it is that Zotero enables such paragraph variable you mentioned. Else I have no idea. Note as I personal feeling that as much as I progress in my investigations, the more I am inclined to switch to more specialized QDA tools (R, Iramuteq, Atlasti for examples among other). Especially when I have to turn back on what I had annotated after a couple of loops in my workflow.
  • Good to know there is a way I can keep the Zotero tags along while creating new notes.

    However, I have a pile of old notes with Zotero tags only which I would like to export to Obsidian.

    Is it possible to insert Zotero tags into the note text while exporting? Or copy the Zotero tags to the note text first (preferably in batch) and export after that?
  • edited October 11, 2022
    Hum I'm not sure it exists a straight way to do that. Maybe you'll need to set up the template and re-create the notes you want to export from your annotations.

    Note that from the last update you coud retrieve the tags you used for your annotations from the general tag panel. So from there you could export the annotation corresponding to your tag. For example I could found all the annotations I tagged as "definition". See the announcement https://www.zotero.org/support/changelog#changes_in_6015_september_30_2022

    Also the Better Note plugin enable some tag selection when creatin a note, using templates, see the discussion here : https://forums.zotero.org/discussion/96945/zotero-better-notes-a-knowledge-based-note-manager-in-zotero#latest

    Last from the same creator, a tag plugin might enable batch edit and tag export. You might want to take a look for your case : https://github.com/windingwind/zotero-tag. This option might be more simpler than the Better note template, though I did not check myself.


  • Just a comment to thank you for your shared template ! I did some little adjustments for my personal needs ! Simple and practical !
  • Nice! Thanks for the feedback :)
  • @alflamingo Thank you so much for sharing!
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