PDF - Zotero - Obsidian: Current state and collaboration for the ONE plugin?

I’ve added the same parameter bibnotes uses, “Bibtex File”, to the Topic Linking plugin. If a valid Better Bibtex JSON file is specified, when the “Extract Markdown from PDF” command is invoked the generated Markdown should have some of the Zotero metadata (title, author etc) embedded. Note this will only work, for now, if the PDF file base name is the same as the citation key (e.g. if I have a zotero entry with the key “foucault1966”, my PDF should be named “/whatever/path/foucault1966.pdf”). I will work on an alternative to this restriction, but the Zotero metadata for now is an add-on, and this plugin should work with / without Zotero.

Oh, I didn’t realize that the conversation was aimed only at getting things into Obsidian or any particular plug-in. I was thinking about the more general issue of “can I use Zotero and Obsidian to write academic articles and output them to Word?”

I also find Pandoc too technical and I don’t use command-line stuff. I currently use Zettlr for Pandoc conversion from Markdown to HTML or Word because it has Pandoc built in.


That would be a great topic as well! Especially if it had lots of sample Workflows from different disciplines…as in

“Here are the steps, templates, plugins, etc that I use for my academic workflow (eg from research to draft article)”

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I really like the LogSeq workflow for pdfs. You have the local pdf open in one pane and a note open in the other. If you highlight a section of the pdf a little pop-up appears and you can click to have a link to the highlighted section added to your note at the cursor position with a copy of the highlighted section next to the link. Later when you are reviewing the note, if you click the link the pdf opens next to the note and scrolls to the relevant paragraph. I would love to be able to do the same in Obsidian.


This is my current capture workflow for PDF into Obsidian through Zotero.

For a non-research workflow where I just want to replicate my standard media->instapaper->readwise->obsidian workflow, this is needlessly complex.


With the move of the iOS app out of beta, this is no longer the case. The app left beta just last week, and it’s been a frustrating limitation throughout the beta. Fortunately, those non-Zotero-stored files are good to go now.

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Are you sure?


If the files are just linked on the desktop and not stored in the cloud somewhere, then obviously the app can’t get to them. I use a separate WebDAV storage with CloudMe instead of the Zotero storage, and I’m able to get to my files. You can go through Settings–>Account to put in file syncing credentials. In the beta, only Zotero’s storage was accessible. Now non-Zotero storage is.


This once occurred to me as well. The reason for me was that I used ZotFile to manage PDF attachments, instead of the Zotero data folder. This means that those files were stored outside the Zotero data folder, which is not supported for syncing PDF files to other devices yet, whether the Zotero official service or WebDAV is used to sync those files.

To convert linked files that are managed by ZotFile, one can use the following method:
Tools > Manage Attachments > Convert Linked Files to Stored Files...

After this, WebDAV can be used to sync PDF files to other devices, e.g., an iOS device.

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Is this workflow for Zotero 5 or the recently released Zotero 6? They handle notes differently. Thanks.

I don’t think the “right-click pdf → manage attachment → extract annotation” button still exists anymore.

After the updating of Zotero 6, mdnotes and zotfile lost many functions.

There is a way to add the right click menu item back via another Zotero plugin called Zutilo, and I believe there will soon be an update with Mdnotes, or the workflow description… (@QuarkQuartet )

Thank you for this workflow; it tells me that I need the bibnotes plug-in. Unfortunately, I use both Obsidian and Zotero on iPad. So there’s a feature to add to the list: Mobile compatibility.

I just came across this topic and am very thankful for that. I’m an Obsidian newbie, so I may have some things wrong. But here are some random observations:

  1. I’m a great believer in the Unix principle that a tool should do one thing, and only one thing, well.

  2. With this in mind, IMHO this discussion conflates too many functions. The most obvious to me is (1) extracting metadata from a Zotero item to create a “source note” in Obsidian versus (2) extracting annotations from a pdf attached to a Zotero item.

  3. The discussion of extracting annotations glosses over the wide variety of ways people annotate pdfs.

  4. One example is a pdf that began life as a physical book or printed journal article and then was marked up with pen, pencil, and highlighter. At a later date, the printed & annotated document was scanned and converted into a pdf. On this electronic document, annotations are intelligible as such to humans but not necessarily to software that expects annotations to have a distinct digital format.

  5. Another example is how some software can only handle some kinds of annotations, even when they are all done electronically. For example, for many years I have drawn straight lines in the margin, parallel to the page’s left & right edges, to identify important points in the document; I use one line for passages that are somewhat important and five parallel lines for extremely important passages. And I do this all on my iPad. Yet I’ve not found anything that can extract the passage as text and the lines as markup. For example, Matthew Meyer’s Obsidian-Zotero-Integration plugin extracts only: highlights, underlines, strikethroughs, notes, and rectangles. In turn, this limited set results from using an external pdf utility.

  6. Since not all annotation styles are alike, any comparison of different software or workflows should include a list of exactly what kinds of annotations and annotation styles are supported.

  7. Cobblepot mentions pandoc, and several other posters mentioned converting Obsidian documents to Word. Again, this presumes what, according to the “do 1 thing well” principle, should not be presumed. For example, I do lots of technical work, and therefore use LaTeX for writing. (Often with the LyX front end.) In this workflow, it’s actually a feature, not a bug, to use an intermediate .bib file rather than import directly from Zotero to Obsidian.

  8. Closely related to this is the issue of the size of the Zotero library. I currently have over 17,000 items in mine. Sure, it’s a convenience to be able to access the entire library, but not at the cost of degrading performance. If I’m writing a paper, I may use only 100 sources to write it, with the final draft having perhaps 50; even a book will typically have at most a few hundred sources. Hence, if one uses a project-specific collection in Zotero along with the Bib(La)TeX plugin, instead of making an Obsidian import plugin search the entire library, one can restrict its searches to the project’s collection.

  9. My workflow is typically (a) initialize a Zotero bibliographic entry, (b) attach a searchable pdf to it, (c) use Zotfile to store the document on my NAS drive (mounted via WebDAV), (d) use PDF Expert on my iPad to download the document from the NAS drive, (e) read, annotate, and markup the document on the iPad, (f) change the name of the annotated document by adding “(marked)” to its end, (g) upload the marked document back to the NAS drive in the same folder as the original, and (h) use Zotfile to link to this second version of the document. This allows me to keep clean and marked copies of the original document, in case, e.g., I want to use one for a class or handout.

  10. This system works quite well, and I see no advantage to using a device that does not allow drawing directly on the screen. If the NAS drive sits behind a firewall and can be accessed over the Internet, the whole issue of synchronization becomes moot. Of course, if a team is working on the project, things become more complicated. But then, isn’t this what git is for?

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With regard to #9, your typical workflow, I would note that the 6.0 release of Zotero was accompanied by an iOS version of Zotero that syncs perfectly. I believe this is the case regardless of whether you use Zotero for storage or your own cloud based solution (though iCloud may be the only supported solution on iOS right now). I’ve been using it this way for the past several months and have been very happy with it. I can grab references either on my PC or iPad, add them to my library, and they’re immediately available in both places. I can read and mark things up on my iPad – including with markings like your 5 hand-drawn vertical lines in the margin – and this mark-up immediately syncs to my PC version if I have it open. I can export the PDF with or without my mark-up, so a clean copy is preserved.

The bit that’s still clunky for me is linking to Obsidian. My Zotero database is actually located in my Obsidian vault, so when I create a new Zotero entry, a folder is created within the vault automatically. Of course it’s named with a not-human-friendly 8 character hash, so I export a YAML record when I first add the reference, which I rename and change to .md. Then I can link freely to that reference in my notes.

Because Obsidian supports hyperlinks directly back to Zotero – which is awesome! – I find that I separate concerns (as a good unix person might) by keeping my highlights in the PDF where they belong, and my notes about the highlights in Obsidian, where they belong.