Zotero best practices

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I haven’t tried this, but I’d imagine you could use Pandoc citations and then use Pandoc coupled with bibtex references to generate fully referenced PDFs. Zotero can export bibtex files.

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Wow! I just joined the Obsidian forum based on recommendations of how friendly the forum and contributors are towards new folk. I am truly impressed and glad I decided to use Obsidian. Thank you for making the time available for such a detailed guide.


I noticed a small bug maybe.
When I am trying to export a single extracted file as markdown, it doesn’t have a link to the zotero back while when I batch export the same thing, it has it correctly.
Could you please check it, if its only me or others as well?

Hi @DummyME! Could you open an issue in GitHub for that? It depends a lot on your settings, so if you can could you add screenshots of them and a GIF of what you’re trying to do to the GitHub issue? Thanks!

Thanks for the thorough guide here. You mentioned exporting everything in one file. However, I haven’t been able to figure out a way to export in a single a file’s metadata and extracted notes. The reason seems to be what is being selected at the time of exporting. If I select extracted annotations then notes are properly exported. However, this means I need to make at least two exports in order to get a file’s metadata and notes.
I submitted an enhancement on GitHub but wanted to ask here in case you know if this is doable.


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Just replied in GitHub, but to summarize here: make sure the Single file option is selected in the settings and use Batch export from the menu.


Thanks a lot for your response. I was able to get the file to export the way I wanted it. Here is a screenshot in case anybody is interested. On top of the configuration you mentioned, I also had to create and modify all the mdnotes template files in order to avoid duplicate or extra information I didn’t want to. In case people are interested, config is: Md Notes Default Template.md and Standalone Note Template files are empty, Zotero Metadata Template is default (plus the {{cloudLibrary}} placeholder, and Zotero. Note Template only has a “## Notes and Highlights” heading and a {{noteContent}} placeholder.

Quick question: I noticed the export creates a double space at the beginning of the file but I can’t control that configuration via template. Is there any way to modify that? Thanks!


@argentum just want to say thank you for the overview and the mdnotes plugin! This convinced me to take my notes in pdf (had been going back and forth) and extract them via zotero to Obsidian’s vault as a literature note. Using the betterbibtex citekey as a title, it also allowed me to then convert a markdown file in Obisidian with the references to the (exported) literature notes to a word docx with active references (via pandoc’s ability to use the better bibtex citeky). This closed the circle for me!
And if I want to exceptionally use a screenshot from the pdf instead of annoted text I can just copy/paste it quickly in obisidian and copy/paste the link back to the pdf in a note, allowing me to have a full, rich view of the literature that I can just keep on quickly overwriting in Obsidian anytime I annotate the pdf again - while keeping the links in Obsidian to that literature note.

So… just thanks!


Thank you for this clarification. For my part, I have the impression that the changes in Zotero Metadata Template have no effect. I stay with the standard template :thinking:

The first two line is from the Default note template which you have deleted blank.
A blank file must contains at least one empty line -> this is the first empty line.
Each template file is separate by one line in the aggregated file -> This is your second blank line.

I resolve this problem by moving the {{title}} from Metadata template to the Default note template.

Hello everyone,

I am new to Obsidian and not long ago I discovered the workflow that @argentum published and that I was also able to provide feedback with Anthony Gold’s interview with Bri Watson. Everything was going well, however, lately I have had problems with exporting the single batch file in MDNotes since it does not appear, but the .md of the annotations does appear.

Note: I have full Zotero storage (free plan), sometimes I restart the plugin and re-create the batch, but the function does not last long.

Greetings to the community

Hi @jcmoral, there was a recent update that made the context menu a bit more context-aware, see here. I also updated the docs over here. If that doesn’t solve the problem, please ping me on discord or open a new issue in mdnotes so we can debug what’s going on.

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Since this is a thread on “Zotero best practices”, I thought I write my question here:

Where do you save your literature notes? In Zotero or Obsidian?

I am right now somewhere in the middle. Some lit. notes are saved in Zotero, others in Obsidian. The ones I saved in Obsidian are connected to projects I am currently working on/interested in. The notes saved in Zotero have contents that “might be of some interest for my future self”. However, I guess I am doing it wrong by splitting my database of notes into two different platforms. What do you think?

@welstand I don’t think there is a one-size fits all solution here, it boils down to what you want to use those notes for. Personally, I don’t write/store notes in Zotero at all. Zotero is primarily a reference manager, it can store notes, yes, but they will be stored away in their database, inaccessible to anything else, not to mention that note-taking there is a bit painful. All those notes will be siloed into whatever reference you’ve attached it into instead of linked to your other ideas.

Obsidian is primarily a note-taking app! It makes it easy to link those “might be interesting” notes with other ideas or problems you might be working on right now! My exported notes go into a folder in my vault (this allows for easy filtering if you want to make clear distinctions). I only send things to my vault if I already have a) read them (and most likely annotated them), b) have a use for them (e.g. I’m probably reading this paper because it’s related to a project I’m working on. If a paper I read is not useful for that project, those notes don’t get extracted & exported).


Does anybody know a way to keep the block reference when re-export a reference from Zotero.

For example: I read and hightlight a paper briefly, extract highlights, export to Obsidian. Then in Obsidian I write my lit note and reference back to each extracted block using block reference.
A month later, I need to come back to the same paper in more detail. I highlight a few more paragraphs, extract and export again, but this time the notes in Obsidian with block reference (^asdf… at the end ) will be overwritten, thus make all the previous link to be broken.

@PhucLe Have a look here for further description of how to organize your mdnotes exports. If you want to prevent mdnotes from overwriting the notes part of your exported file, you have to configure your export behavior with the “split files” option.

Yet, in your case, you actually want your notes/annotations to be overwritten - in a way that they become updated/amended when re-exporting them. I think this is not possible with the mdnotes plugin so far.

I recommend using the prefix/suffix option - that’s at least what I do in order to prevent unwanted overwriting of content: configure mdnotes to name your exported file like, for example, {citekey}-zoteroexport. Once you start working with your note in obsidian, making changes, amendments, adding comments etc., rename it to just {citekey}. Now, whenever you refresh any export from within zotero, nothing will be overwritten - but instead kind of “amended” to your working note.


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

This is coming up in a future update of mdnotes.


First and foremost, thank you for this amazing plugin

I have one problem, if you could help please, I have been hours at it and still can’t make it work like you did I am sorry for my lack of understanding and would truly appreciate yours or someone’s input

This step, would like the labels addition:

Setting extensions.zotfile.pdfExtraction.colorAnnotations to true, will add the color as a background in the annotations, and you can use %(color_category) to add labels in extensions.zotfile.pdfExtraction.formatAnnotationHighlight according to the colors in extensions.zotfile.pdfExtraction.colorCategories

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Hi @PedroSilva, Zotfile’s colores annotations are not mutually compatible. Are you splitting the notes based on color too? That might be why it doesn’t show up. Feel free to ping me on Discord and I can help debug if you want.

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