Zotero plugin to export metadata and notes to markdown

Hey all,

I was wondering if anyone could give me any guidance. I have installed Zotfile, made relevant notes/highlights and extracted annotations into a note in Zotero. But I cannot export that zotero note to markdown, no option is available upon right click.

Is there something I have done in the install? I have removed and re-installed but same issue.

Running off Mac BigSur 11.1

Thanks in advance!

Hi @Dan_Martin77! You have to install the mdnotes plugin for that (it’s not part of Zotfile).

Thank you so much. How naive of me.

Appreciate your support/patience!

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It would be great to have notes auto exported from Zotero and auto-imported in Obsidian. Anyone have some ideas on how to do this? I do not want to go through the entire process of exporting, saving in a location, then opening them and copying them into obsidian.

Why don’t you export directly to your obsidian vault? (That’s what I do). No way to automate the extraction, that I know of, but you can for sure reduce the number of steps so it’s barely noticeable.

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I’m having an issue that is just baffling me. I’ve just set up mdnotes along with Cat’s suggested workflow, and it works except that the exported annotations don’t include blockquotes. I’m running the current beta of Zotero and the dev build of Zotfile, which I figure might be causing the issue, but if there’s something I’m missing in the config I’d really appreciate the help.

Are you using the latest mdnotes build (alpha4)?

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Aha! I was on 0.1.3; just downloaded alpha 4 and blockquotes appear to be working. Thanks for the help and the excellent plugin!

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On my export Im not getting the page of the annotation linked. Im using the zotero-beta pdf tools.

You won’t get links with the Zotero beta. Please see Zotero with integration of pdf.js - already available in Beta - #2 by argentum


Hi, newbie here.

I managed to get zotfile to extract notes by color in Zotero via Manage Attachments > Extract Annotations following your post, yet I can’t make it work via Mdnotes > Extract to markdown. Nothing happens.

Using last zotero version in windows 10.

Plus, how should I set the default folder directory to export the markdown files for it to be the same folder the pdf is set in?

Thanks a lot!

Which version is that for you? Is it the alpha version linked in the releases?

This is not currently possible! If you’d like this, please open an issue on the repository so I don’t forget!

Hi, I managed to get it to work! It was my fault by not understanding that I should first use Zotfile to get the notes inside Zotero via Extract Annotations and then use mdNotes to create the Batch Export. I was assuming the second already covered the first action, my bad.

Regarding the folder directory thing, I opened an issue in Github as you requested.

Thank you!

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Hello @argentum,

First of all, THANK YOU for this wonderful plugin!
I’m not sure if this is the place to ask for new features (sorry if not), but would it be possible to set different paths for the mdnotes generated files? It would be marvellous if I could automatically send the metadata and extracted annotations to a folder separate from my literature notes folder.


Happy to hear it’s been useful for you! For feature requests, it’s usually best to add them as GitHub issues! I’m almost sure someone asked for something similar, but if you add a comment it lets me gauge interest and take it into account in the way I prioritise requests!

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I’ve just started to use the plugin, it’s really cool! Thanks!

Question: There is some way to change the template? I would like to move some things to the frontmatter

There is, you can find that in the docs: https://argenos.github.io//zotero-mdnotes/docs/next/advanced/templates/defaults

Cat’s workflow also covers that a little bit: Zotero -> zotfile -> mdnotes -> obsidian -> dataview Workflow



Thank you so much. I had the same problem and just updated the mdnote version. It literally just blew my little mind. :grin:

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