Setting up Zotero as a reference manager, and Obsidian as a note taking app for references downloaded in Zotero.

Setup

1. Install Zotero.
2. Sign in and wait for sync, this might take a sec. You can click the icon in the top right to force a sync if it’s not happening automatically.
3. Download latest release from here and then in Zotero -> tools -> addons -> install addon from file, install the thing you just downloaded.
4. Restart Zotero, and then click through all the default settings for Better BibLaTeX
5. In Zotero, File -> Export Library -> Better BibLaTeX

6. Save the exported file to somewhere (e.g. Obsidian vault).
7. Install the Citations plugin in Obsidian (community plugin), and then point it to the .bib file exported from Zotero.
8. Customize the folder name which is supposed to hold notes, and make sure you create the folder, otherwise you’ll get weird ENOENT errors.
9. Customize the title to remove the @ because that doesn’t belong in filenames, and then change up the template slightly.

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---
title: {{title}}
authors: {{authorString}}
year: {{year}}
---
Published in {{containerTitle}} online [here]({{URL}}), local copy in Zotero [here]({{zoteroSelectURI}}).

# Abstract
{{abstract}}

# Notes

10. Use Ctrl + Shift + O to open (or create if needed) the reading notes for a specific citation. Ctrl + O will open existing files only, which is convenient for letting you go back to things you just had open.

Workflow

1. Download a new paper via Zotero Connect to get it into your library.
2. Open up Obsidian and use Ctrl + Shift + O to create the new reading notes for the paper.
3. Click on the link in the top of the newly created note to take you to the Zotero citation for that paper.
4. Open the paper and start reading it in the built-in Zotero PDF viewer.
5. Highlight details in Zotero itself.
6. Copy important information, thoughts, and figures into the Obsidian document.

Obsidian Sync

I also purchased Obsidian Sync as part of this setup. The vault syncing works pretty well, but I had some trouble getting the settings sync to work. It looks like the second machine I set up with Obsidian overwrite the settings in the vault, but I was able to use the version history to restore the correct settings. Also, settings only sync on boot, so restarting Obsidian was required.

There’s a limit of 10GB per vault, of which I’ve currently filled ~80 MB of. Most of that comes from the .git folder, which I could definitely remove from the sync if necessary. Image below from TreeSize Free.

Sources

• This guide from Mariana Montes
• Notes on settings from Obsidian