Creating nice markdown exports with annotations

davemurrayrust

I used to use MDnotes for exporting citations to Obsidian, and I'm trying to recover similar operation in v6. I'd like to be able to have notes that I export that include all the bibliographic information and highlights from the PDF. At the moment, I can
- do a 'Create note from Annotations' command to make an annotations note
- do a MDnotes -> Create full export note to get the markdown file out.

It works, but there are a couple of issues:
- the note from annotations is not kept updated; if I make a new one, they are both updated, so I have to delete the previous one
- The MDnotes annotation template doesn't allow for newlines, so all the annotations run together
- I miss the ability to have the annotations link back to the source of the annotation - is there any chance of having these tags link back to the original source

Also - is this still the right way to do things? I've seen the Zotero Desktop Connector, but I was hoping not to have to run something else. I've also seen references to native Markdown export, but I can't see a way to do that - it's not in the export formats AFAICT.

Thanks!

hsiangyu_wong

No offense to the excellent work of the Zotero developers, but it seems like my plugin Zotero Better Notes(https://github.com/windingwind/zotero-better-notes) fits the export and auto-sync need.

You could export the notes to markdown(including images, links, and math) and keep the .md files in sync with the latest version of Zotero notes. Check the syncing notes in File -> Better Notes Sync Manager.

dstillman

I've also seen references to native Markdown export, but I can't see a way to do that - it's not in the export formats AFAICT.

@davemurrayrust: I'm not sure what you're looking at, but the default Markdown note export certainly includes links back to the item and the PDF annotation. You get Markdown as an option if you right-click on a note item and choose Export Note… or if you use Quick Copy on the note with your Quick Copy Note Format set to Markdown + Rich Text (as it is by default). Rich Text doesn't currently include the links, so if you paste in rich-text mode, you won't get the links, though we'll be adding an option for that soon. (You can hold Shift when dragging a note to Obsidian to force Obsidian to paste it in plain-text mode.)

It doesn't auto-update an external file, though.

davemurrayrust

@dstillman - That's what I would have expected, but Markdown is not in the list that I get either for right clicking on an item and saying Export Item or in the Item Format: dropdown for Quick Copy (Zotero 6.0.10).

I'll try 6.0.11 and see if that makes a difference - checking for updates hadn't flagged that there was a new version.

Edit - nope, still nothing: https://imagebin.ca/v/6pindJvcxr3B

Is there anything that I should have configured to make Markdown export be there?

davemurrayrust

@hsiangyu_wong - that looks very interesting, I'll check it out

dstillman

You appear to be looking at the export format list for a regular item, not a note.

And, as I say, it’s the Note Format setting in the Quick Copy prefs, not the Item Format.

davemurrayrust

Ah, OK, my mistake!

Does that mean there is not a way to export everything - bibliographic information and highlights to one Markdown file without using MDnotes or similar? Or to pull all the PDF annotations into a note automatically?

Thanks!

dstillman

Zotero 6's built-in Markdown note export doesn't do anything with item data, no. That's a use case mdnotes addresses (though I don't believe it gets much development).

To be clear, if you're using Obsidian, using a plugin specifically built to provide Obsidian integration would be a reasonable thing to do. (It's not called "Zotero Desktop Connector" anymore, by the way — that was a confusing name that we asked the developer to stop using. The official Zotero Connectors are something totally different.)

We're always open to feature requests that would be generally useful, but plugins are a feature, not a bug.

We have discussed the possibility of adding the ability to quickly update a single, unedited note with all of an item's annotations without needing to create a new one and delete the old one.

davemurrayrust

I'm now using BibNotes in Zotero (it's hard to tell which has more community love between that and 'Obsidian Zotero Information').

It works well, except for that last point you mention about having to delete and recreate the Annotations file. Everything else seems to be quite lovely.

Thanks!