From Zotero, select the reference you want to export. Right-click to pop up a context menu and select “Export Item…” about 2/3rds down the menu. This will open an “Export…” dialogue box, which at the top has a list box labeled “Format:”, which has ~20 different export format options. None of these are markdown, as far as I can tell, so I select “Better CSL YAML” and hit OK. If I then change the extension from .yaml to .md, I can open, edit, link, etc in Obsidian.
Why can’t there be a better built-in PDF reader and annotator in Obsidian? This would close a lot of the loops with the whole Zotero-to-Obsidian workflow. Just read and annotate PDFs directly in Obsidian, and then extract the highlights directly into Obsidian. Not sure why such a plugin hasn’t been discussed more
For academicians, we need the full suite of citation management functionalities and I am not sure obsidian’s dev time is best spent replicating otherwise relatively mature products like paperpile or zotero instead of ensuring obsidian interoperates with citation managers.
This thread is great, but, so far, it doesn’t really deliver on the second part of its title: “collaboration for the ONE plugin?” I guess that answers the question mark after “ONE plugin”… it is extremely difficult to build the one plugin that most people will be happy with. And there is nothing wrong with having many plugins around.
What makes the current situation somewhat confusing for anyone trying to figure out their own workflow is that
there are two apps involved (obsidian and zotero), each with their own plugins and features, so that it is not the easiest task to wrap your head around which tasks you should best do with which app/ plugin.
Zotero 6 has rendered many workflows documented on the net obsolete and it is not always evident which ones. It’s probably a good idea to treat any tutorial that doesn’t mention zotero 6 as obsolete (though, technically this is not necessarily true).
I am not sure what exactly the intention with the (yet unfinished) Obsidian Zotero Plugin is but since it seems to include both a plugin for Zotero and one for Obsidian, it looks like a promising project because maintaining both ends of the bridge in the same project probably makes things a lot easier for the user.
But what about the Zotero Integration plugin? Why hasn’t anybody mentioned it here? It has less than half the user-base of the citations plugin, but it is still significant:
Another plugin that might be worth mentioning here is Zotero-markDB-connect, which - in zotero - provides links to notes in obsidian.
The final thing I want to mention is a feature of Zotero itself that is easily forgotten when we talk about various plugins: Quick export. You can use it to simply drag and drop an annotation from the Zotero pdf reader into Obsidian and it will give you the annotation text + comments together with a reference to the source. If you hold shift while dragging and dropping, the reference will include a (deep-)link to the page of the pdf which, when clicked will open the annotation for you in zotero.
When I found out about this gen, my first thought was: do I still need any plugin now? Answer: yes, for references, but probably not for annotations. - It depends on how you work with annotations. If you simply want all annotations/highlights in obsidian, then a plugin is the way to go. But I’m trying to get away from hoarding highlights that I’ll never look at again, and instead distill from those highlights what I really want to keep in obsidian. And for that, dragging and dropping notes into obsidian seems like the best way forward.
Zotero is, then, a repository for notes and annotations that I made while reading and I can bring them over into obsidian once I actually want to do something with them.
I would like to have a full citation imported with the metadata section so that I can quickly copy it without having to go back to Zotero or another program to get it. Not in the sense of a reference manager, but because I might be composing an email and want to share the full details of the reference, or as part of a lecture draft.
I recently noticed the Pandoc Reference List plugin which is really great for having full citations at hand inside Obsidian while working with much shorter citations and links inside the markdown documents themselves.
It does rely on pandoc in the background, and kind of creates a bibliography in a separate sidebar pane similar to the local graph of a note.
As long as you do not need to regularly use different reference styles, this plugin makes it very easy to share references directly from Obsidian
Update on the obsidian-zotero project: the first public beta of obsidian-zotero-plugin is available for testing! The document isn’t complete yet, but you can find the installation guide here if you want to try it out: Installation | Obsidian Zotero
This is amazing. Everything seems to work smoothly. Excellent work! The annotation view is great. And I can’t believe that the annotation in obsidian updates when I change it in Zotero. Just like that, without me doing anything. (Comments and tags are not added after the fact, though - is this planned?)
But I there are two things I don’t quite understand:
What does the Zotero add-on do? I installed the obsidian plugin and it worked like a charm without me even touching Zotero. Then I installed the Zotero add-on, but I don’t see any difference.
What are the BlockIDs for that are shown next to the page number for each annotation?
The Obsidian-Zotero plugin from aidenlx is really really neat!
It will be nice to see it once it’s even more refined:
More customization of the output format, such as the option to block quote instead of code block, or information on how to refer to specific Zotero attributes
My only other pain point at the moment is in merging with literature notes that already exist
I think the Zotero add lets you click from Zotero into the related Obsidian note? (I haven’t used it though)
I suspect the block ID is to have a unique identifier for each annotation, say I had three annotations on page 2 of the PDF, the block ID will let me refer to each from within Obsidian. I don’t particularly like having the block ID, but I don’t see a great way to uniquely refer to the annotation either…
That would make sense. And I did find an item “Open in obsidian” in the context menu of zotero items,
and clicking it brings me to Zotero but doesn’t open the corresponding literature note.
I also see that link in the 3-dots-menu of annotations:
It also opens obsidian but not the note, let alone the annotation.
Maybe it’s simply not yet fully implemented…
Obsidian supports block-level references by default and it creates that unique identifier once you refer to a specific block (i.e. annotation). So for that there shouldn’t be a need for those IDs. Besides: the IDs are “attached” to the heading for each annotation, not for the annotation itself, so that you can only use it to refer to the heading, not the actual annotation. And to refer to a heading, you don’t need any ^ IDs at all because you can refer to headings directly.
Here is an example (ignore the #3, I don’t know who put it into my screenshot ) :
So, here I’m creating a reference to a literature note called Follet1919, by pressing ^ I open up available blocks to link to in that note, and as you can see, the annotation “The creative power …” is available as a block reference (#1). And so is, of course, its heading “Page image 2” (#2), but not because ot has a ^ ID but because it is s
also a block like any other.
I guess we’ll understand better as the documentation evolves…
After checking this and several other options out, including Logseq, Okular, the browser version of Hypothes.is, and landed on two applications
The first one is Liquid Text, it’s a very visual orientated annotating software that allows you to work on a canvas where you can drag and drop annotations that serve as links to their sources within the PDF. It allows export directly into the pdf as regular annotations and adds up the canvas as pages at the beginning, or export as a .docx document with the list of notes, if you get the premium license you can draw to connect things within the document and the canvas (as well as other PDFs). I am satisfied just with the free version, and am considering getting the license although the Windows version is really bad quality (because it’s originally an iPad software)
The second is Memex, as a web browser plug in, works pretty much like Hypothes.is, but it feel nicer, it has an option to export all notes from a source as markdown that you can customize, and my favorite thing, it supports easy YouTube video annotation with timestamps, so now it is extremely simple for me to just take a note on a video and have it immediately on my vault with all the links and formatting already in place
I love this update! It solves one of my eternal pains, which is seeing my colour-coded comments in Obsidian and making the annotations searchable! Thank you so much for working on this!
Some remarks, with the first one being the most critical for me:
It would be great to have the “Zotero Annotations” window remember in which document note I was last, so I can continue to write on my note while having the annotations on the side - now they immediately disappear when I click into another note). This and having the Literature note open in a new tab rather than the current one would greatly increase the workflow !
It is important to know that the note itself is not updated, only the annotation view window. This is not a problem, but one must be aware that only documents with the final title, author and completely done annotations (!) are to be added into Obsidian if that information should be searchable (e.g. I put hashtags into the annotations like #citeThese/ClimateCatastrophe to identify interesting papers)
The newly created note itself is of limited use to me: The order of annotations seems to be random, rather than chronological (issue 1) and is very hard to read due to unnecessary lines (issue 2). For me personally, this could be much slimmer, without headings and with the single comments being bullet points/comments tugged in (like in this post)
Also, the external “attachment” link results in an error, not sure what is supposed to happen
I’ve had the same problem with Quick Switcher, and could not figure out how to make it work. The citation key did not return anything either, the matching seems a little wonky. Did you manage to find a way to influence the results?
I made a beginner user’s guide for the AidenLx Zotero plugin by distilling all available documentation I could find and some trial-and-error. Please check it out here and provide me with any feedback or additions you think would help. Thanks!
Could you explain some more what bibnotes is better at?
I suppose those plugins that don’t tap directly into the Zotero database should work on mobile (provided that the exported zotero records are in your vault). So that would be Bibnotes Formatter (which uses a JSON file exported from Zotero) and Citations (which uses a bibtex file exported by Zotero).
As I think about it, that might actually be a reason to use two plugins: one for mobile and one for desktop.
Performance
Full access to Zotero data
Highly customizable templates
Annotation View
Annotation import
Create literature notes with ease
) :
