Zotero best practices

[christian.junk]

Thank you very much for this great summary. Can you please elaborate more on bullet point 7. You are mentioning the “inbuilt printer of obsidian” but I haven’t found this feature yet. So far I use Marked2 with pandoc as pre-processor.

Regards,
Christian

[welstand]

Is there a way to cretae a “Quick Copy” format in Zotero to export (in Obsidian, of course) both reference and item link? The result should look like that:

[Badiou, Alain. *Ethik: Versuch über das Bewusstsein des Bösen*. Translated by Jürgen Brankel. Wien Berlin: Verlag Turia + Kant, 2015.](zotero://select/library/items/INX5ZN8A)

In this way, you have a clickable reference, which would be for my purposes simply AMAZING.

[Sans]

Hey all,
I was wondering if there is a way to skip the need to save the annotations to a dedicated file.
In my usual process I highlight/comment the PDF, then extract annotations, then export the same annotations to a .md file which I then have to open in order to copy and paste its contents to Obsidian (and then I have to manually delete the file).
If there was a way to send the annotations to the clipboard, this would save me a lot of time, given that this process is repeated for dozens of reference notes.
Maybe there’s a setting I’m not aware of somewhere…?
Thanks

[argentum]

@Sans why wouldn’t you save the file directly to your vault? Maybe I’m missing a bit of context

[y.h]

You could also save the .md file directly in a folder in your vault (this is what I do)

[Sans]

@y.h I didn’t think about it. This is possibly the solution I was looking for!

@argentum I am just stupid

[tb87]

In case anyone was looking for an (author, date) version of the plugin:

{
	"translatorID":"8dbf9b92-f796-4153-8f2e-ac6c157500dc",
	"translatorType":2,
	"label":"Markdown Item URI",
	"creator":"Silent",
	"target":"markdown",
	"minVersion":"2.0",
	"maxVersion":"",
	"priority":200,
	"inRepository":false,
	"lastUpdated":"2020-11-30"
	}
	 
	
	function doExport() {
		var item;
		while(item = Zotero.nextItem()) {
			var date = Zotero.Utilities.strToDate(item.date).year;

			var year = date && !isNaN(date) ? " " + date : (typeof item.date == 'undefined'?  "" : " " + item.date);
			var library_id = item.libraryID ? item.libraryID : "";
			var author_lastname = getValidAuthor(item);
			var title = item.title ? "*" + item.title + "*" : "";
			var key = item.key;
	
			Zotero.write(`[(${author_lastname},${year})](zotero://select/items/${library_id}_${key})`);
		}
	}

	function getValidAuthor(item){
		if(item.creators && item.creators[0] && item.creators[0].lastName){
			return item.creators[0].lastName + "";
		}else{
			return "";
		}

	}

[janisc]

@argentum

@PhucLe I have teased this in Discord, but not yet here:

This is coming up in a future update of mdnotes.

Hi @argentum , this figure is exactly what I want! Particularly, I’m interested in the block IDs, I mean adams1979-78f7565. Do they come from zotfile/mdnotes? Are they fixed after each extraction from pdf to md files? Could you point me to a reference where I find instructions on setting up zotfile for these IDs?

[janisc]

As @argentum commented on discord, this is a feature of mdnotes and it’s described at https://argentinaos.com/zotero-mdnotes/docs/next/advanced/hidden-prefs:

• Setting extensions.mdnotes.obsidian.blocks to true will append a block ID to all non-header text blocks of exported Zotero notes, i.e. to each highlight and annotation extracted by Zotfile.

[Kullenej]

In the latest beta version of Zotero and the new pdf-reader, you can export the annotations as md-files with working zotero-links. Just a head-up.

[Marc-A]

@Kullenej Great news! Thanks for letting us know. The function is excellent and works well – it’s a little tucked away but in the expected place. [Select Annotation ] > Right Click> Export Item >Select Markdown option.

[janisc]

Hi @Marc-A, could you tell me which version of zotero you use?

I just re-installed the latest zotero beta (5.0.97-beta.57+07df7d0de for Linux64) from dev builds. When I right-click on an annotation, unfortunately, it doesn’t display a markdown option.

[Marc-A]

@janisc Using 5.0.97-beta58 on macOS. It looks like the function you’re missing was only added a few days ago. I’m sure it will be there in one of the next Linux updates.

[warguelles]

Just in case someone has missed it:
With the new “Markdown export of notes” functionality of Zotero beta-pdf reader, it is not necessary to import your notes through an MD-file… You can also drag-and-drop them into a note in Obsidian (pressing Shift key during drag-and-drop will keep links back to Zotero items and individual annotations).

[Archie]

can someone please explain it to me how this new system works step by step? I was using the old zotero zotfile mdnotes a while ago and then new pdf reader came and suddenly nothing was working and I waited for this workflow get fixed.
last i tried (which was like one or two weeks ago i think) i could not extract highlights added with new native zotero pdf reader via zotfile

[tomhaley]

The Zotero beta reader does not store annotations in the PDF so Zotfile can’t see the annotations. You can force Zotero to write the annotations to the PDF (with a PDF open in the Zotero viewer, select File->Store annotations in file), at which point you can no longer edit them in Zotero. However, other changes to the Zotero beta have occasionally broken mdnotes so even with annotations stored in the PDF you may have to find other workarounds.

I believe the author of mdnotes has stated they’ll likely update once the new Zotero is out of beta. Zotfile’s maintainer has said they don’t really have time to work on it, and given that some of the main features of Zotfile are basically superseded by the new Zotero, I wouldn’t bet my workflow on Zotfile for the long-term.

The latest version of the Zotero beta does extract annotations and can then export them to Markdown. It’s pretty cumbersome (you have to select “Add Item Note from Annotations” from the Item Notes sidebar and then right-click export the note from your library), but it’s something.

[argentum]

Correct! See here:

Zotero with integration of pdf.js - already available in Beta

Pasting part of my reply from New Native Annotations in Zotero (Currently on Beta) · Discussion #77 · argenos/zotero-mdnotes · GitHub : I took a little time to set up a profile to test with the beta over the weekend, and the beta simply has too many limitations currently. I’ll add my summarized comments from discord and other issues below. As you say, this will likely be addressed later, and I remain to be convinced that the annotation lock-in is worth it. The main limitations I found: Limi…

[warguelles]

Some functionalities are still missing in the beta, but IMHO the most important advance now is that you can work with the Zotero integrated PDF reader. I liked it so much that now you can export annotations and your notes via drag-and-drop into a note in Obsidian (pressing the Shift key during drag-and-drop will keep links back to Zotero items and individual annotations in the PDF document).

The ability to export graphs is, by now, a great missing!

[dae]

I just released a minimal Zotero add-on that may be of interest. It lets you open existing Obsidian reading notes from the contextual menu of Zotero items.

ZoteroObsidianCitations searches your Obsidian Vault and adds a tag to the corresponding items in your Zotero database. You can color this tag so that Zotero items associated with Obsidian notes are visible at a glance.

It’s at an early stage of development so let me know if it doesn’t work for your use-case, if you find bugs, or if there are other features you’d like to see.

E.g., in this image, the blue marker shows which items I’ve made Obsidian notes for

[y.h]

I love this! I love the synergy it creates between obsidian and Zotero :).
I will try it out this week, and I will let you know if I have any feedback to give.