Zotero best practices

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. :frowning_face:

@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.

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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).


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

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has said they don’t really have time to work on it, and given that some of the main features of Zotfile are basically superseded by the new Zotero, I wouldn’t bet my workflow on Zotfile for the long-term.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.


Correct! See here:

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!

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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.

Zotero-MarkDB-Connect 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


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.

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So, the zotero → edit pdf → extract to zotfile → paste to obsidian with zotero links is interesting, but I was disappointed to find that things break down if you try to then paste the obsdian doc into Word, since Word specifically uses the zotero plugin that has a ribbon button.

However, I think a simple macro would be usable for finding and converting these zotero links into the word bibliography.

For example: Note text I want to include (note on p.1)

The macro would find all zotero links, call the zotero word plugin for each instance, and add the relevant word citation using that plugin.

For example:

Note I want to paste into word (note on p.1)

  1. Run macro in word
  2. Macro finds each instance of a zotero :// link
  3. Parses the link, finds an attribute
  4. opens the zotero plugin dialogue, pastes in the attribute, hits enter
  5. Zotero plugin generates the dynamic word links and bibliography using its existing capabilities.

I know this probably seems like a roundabout way to convert obsidian notes with handy zotero links into working citations in a word doc, but it could be useful for the zotero workflow. As far as I can tell, the zotero plugin is the only way to add the zotero items to a word biblio, but it doesn’t use the links; but a simple macro wrapper could tie the two together.

No need to paste, you should be able to save in your vault directly.

The workflow isn’t really meant to help there. I recommend using pandoc to covert to word in that case (at least for markdown → Word).

Hey, I just tried out this plugin and I’m loving it so far. Enabling a two-way integration between Obsidian and Zotero is fantastic. Great work!

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glad to hear :slight_smile: thanks for reporting back

I love this workflow, especially since it appears it can work with most any PDF annotation as well as Zotero’s own beta reader/annotator. However, my ideal workflow would be being able to add annotations to a Zotero PDF (via beta reader and/or from pre-existing, imported annotations), then have all those annotations automatically saved into a destination annotations markdown file (one per PDF, perhaps with an author-date title) within an ‘annotations/’ directory in my Obsidian vault, quotes and pdf page links and all. I could then link to or transclude the MD annotations from any other notes in my vault. If I subsequently added new annotations to the PDF (or removed old ones), those annotations would be automatically added (or removed) to that same annoations MD file in my vault, without breaking any Obsidian links to other annotations in that file. I don’t want to have to think about exporting my annotations or moving them over - I just want to highlight something in a PDF, then know that I can find that highlight in the corresponding MD annotation note.

The Annotator plugin already allows some of this idea (GitHub - elias-sundqvist/obsidian-annotator: A plugin for reading and annotating PDFs and EPUBs in obsidian.) but it’s still in earlier development and having Zotero integration would be amazing.

Does this ideal sound plausible, or even interesting to anyone else? I am not sure if the mdnotes plugin could even do all this or if Zotero itself would need changes. EPUB annotation too would be even better, but I know that ain’t happening :rofl:


Check the bibnotes plugin :slight_smile:

It does not import annotations automatically but it does simplify the process a bit IMO.
You can also update annotations when you make new ones, although there are still a few bugs left.

e.g., updating annotations (syncing with zotero) works but the newly added annotations are added with a missing return line; so you have to add that manually. If you do not, subsequent updates won’t be possible.

You could also comment on this feature request on the zotero forum : [feature-request] Update extracted highlights - Zotero Forums

**I do hope somebody will come up with what you are hoping for :smiley: **



First, I apologize for taking so long to reply. I was not monitoring this forum, but I expected to be notified by email of replies like yours. Either I missed the email, or it never came.

Second, I’m only now rolling up my sleeves and learning to use Obsidian in depth. So take what I say with a grain of salt. Nonetheless, my answer to your question is an emphatic NO!

tl;dr Don’t store files with generic file types in application-specific locations unless the application organizes and maintains these files in an intuitive, transparent way for general access by any other application that might be used to work with them.

Here’s why. Certain file formats are designed to be “open,” which means various different programs can use the same file format. The *.md files Obsidian uses are an example. Other formats are “proprietary,” and typically can be used only by the owner of the format or one of their licensees. Adobe originally developed the PDF format, but released it as an open standard in 2008. This is why so many applications, including open-source applications, can now create, access, and otherwise use PDF files.

As a general rule of thumb for organizing open- or generic-format files, I try to store them where I can logically find them. E.g., research-related files are stored in ~/Documents/Research/*. If multiple application programs can use a particular file type, I either keep this type of file in folder(s) dedicated to a specific purpose and/or a general, application-agnostic folder . For example, I keep PDF files of my tax returns in “~/Documents/Personal/Financial/Taxes,” but I store all scholarly PDF files on my (mounted) NAS drive in myNAS/mnt/Volume1/Documents/ZoteroLibrary.

At first glance the folder name “ZoteroLibrary” might seem to contradict what I said about application-agnostic folders. But I use the Zotfile Zotero plug-in to maintain the library, and the plugin names the files according to a user-specified convention (e.g., “Author Date - Title”) and then simply uses the native file system to organize the PDF files. Any other app can find and open the file by simply following the appropriate path, e.g.: “myNAS/mnt/Volume1/Documents/ZoteroLibrary/AdamsP/AdamsP 1998 - Network topologies and virtual place.pdf”. To access the file one could either know its absolute path or (using Finder, shell commands, or another file navigator) navigate to the folder and access the file.

Zotero & Zotfile organize my PDF files in a logical structure that can readily be used by any app that can read PDF files. This includes Obsidian. But Obsidian’s file organization is designed for note-taking, not library maintenance. Anyone using Obsidian’s vault structure would have to know details about what and how Obsidian does things. IMO, it’s best to avoid such application-specific conventions unless they are what ordinary humans would ordinarily do anyway.

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Hi, there,
I would like to ask if you still use the “highlights” PDFs reader?

how you manage to extract the inline notes separate from the highlights? or you use the “comments”?

Thank you very much!

This is very useful! Thank you for sharing!

Can I used that on IPAD pro? It realy very helpfull …. Thanks

Did you, or anyone else, try out Protolyst yet?