Zotero -> zotfile -> mdnotes -> obsidian -> dataview Workflow


Sorry for not replying before (I do not visit this forum often). I’m packaging my script into a plugin, so I should be able to share it soon

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First, thanks for such a detailed explanation. I’m having trouble following how to get colored annotations into Obsidian.

I basically use two colors - yellow and cyan. How can I extract both into one annotation file that I can then export to markdown?

Hi, thank you so much for this workflow, I’m loving it so far! I had a query about the backlinks used in [[Important]] for example with the highlights - what do you do with them once in Obsidian? Do you create a separate ‘Important’ md note?

Thanks very much for this posting this workflow!

Regarding the setting of extensions.zotfile.pdfExtraction.formatAnnotationHighlight, I wonder if it is possible to add a fixed ID/identifier to each highlight. Then, it’ll be easier to do block reference.

Although obsidian will automatically generate a block ID for us, this ID is changed after each extraction from zotfile/mdnotes. And then all links pointing to our highlights will fail.

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In case anyone else asks the same equation again: Zotero best practices - #179 by janisc mdnotes is able to generate a unique block ID for each highlight.

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That’s great. Looking forward to your plugin. Keep us posted!

Thanks very much for sharing this workflow! I’ve learned much from both the post and replies.

I’m new to Obsidian & Zotero, so the following question may be dumb to you guys. I created a new placeholder according to the guide, but how to change the Preference Name or to delete the entire entry? And where could I find all the field item names and their usage? I googled and found this page (kb:item types and fields [Zotero Documentation]), but still got confused.

Thanks in advance.

Thanks for the great workflow!

I use a lot of subcollections in my Zotero organization. Is there a placeholder that exports the parent collections?

I have uploaded the first version of the plugin today (BibNotes Formatter: New Plugin to Export and Format Annotations from Zotero into Obsidian)


11 posts were merged into an existing topic: BibNotes Formatter: New Plugin to Export and Format Annotations from Zotero into Obsidian

Awesome, thanks a lot.

When I got to the config editor in Zotero and change the values in extensions.zotfile.pdfExtraction.colorCategories nothing changes when I extract annotations. they still show the same colors from before. Any suggestions?

Whenever I try to change these default settings and export to Markdown using mdnotes, the markdown files are never made. When I hit the option to export to markdown, I get the popup of where to save it and select it, but then nothing happens.

How do you think this work flow compares to the one I found here?

Is it just me, or do all workflows utilizing Mdnotes with Zotero’s highlighting and annotation system in Zotero 6.0 generate some ugly html with the annotations?

Or is it the default Mdnotes template that’s causing this?

I am attempting to implement the (seemingly underrated / underdiscussed) Obsidian Zotero Integration Plugin to get around this, but I’m also having trouble making a template look decent with that.

This workflow doesn’t work with zotero annotations, afaik, only with annotations in the pdf itself. (@argentum could possibly address that better, since I use Juris-m which hasn’t yet updated to version 6).

As I see it, most people are switching to the integration plugin or the Alfred workflow. None of these Workflows is perfect, so it all depends on what your priorities are.

Mdnotes does a good job of separating colours and extracting text accurately with correct page numbers but fails at auto-updating with new annotations (you have to re-export, meaning loss of block ids).

Alfred works well with page numbers and extraction but fails at colour categorisation.

Zotero integration works well at automation, colour categories and updating new annotations but fails at page numbers (but that is apparently taken care of if you use the in-zotero annotations).

You could also join the discord server, where there’s a dedicated thread for the integrator plugin, along with plans for The Annotation Plugin to Rule Them All.


If you upgraded to Zotero 6.x, you will find that the “Extract Annotations” feature is done by the Zotero built-in functionality. See these two links

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I love Zotero and have used it for some years now. I don’t know that I’m going to link it to my Obsidian, but the presence of this functionality is mind-blowing to me. I also learned some things I didn’t know about Zotero.

Hi all, any updates on this workflow to successfully pull color annotations as of 20220811? I have tried this with the settings given in Cat’s original tutorial and followed through the issues in the thread–nothing is working for me in pulling the colors of highlights. I am able to get all the annotations out no issue (right click on PDF, “Add note from annotations”), but I may be missing something fundamental in settings or there has been a software update in one or more components. If you have any ideas on how to fix, I’m all ears!