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zotero

zotero

Zotero is an open source reference manager.

Install

Download and install Zotero from the official website or

Ubuntu

zotero-deb provides packaged versions of Zotero reference manager and Juris-M for Debian-based systems.

curl -sL https://raw.githubusercontent.com/retorquere/zotero-deb/master/install.sh | sudo bash
sudo apt update && sudo apt install -y zotero

Windows

chocolatey:

choco install zotero

winget:

winget install DigitalScholar.Zotero

Attachment files management

In the Zotero free plan, the storage space for attachments is limited to 300MB.

Use WebDAV

Free online storage spaces supporting the WebDAV protocol.

In Zotero settings

  • Sync => File Syncing, enable sync attachment files in My Library and choose WebDAV. Follow the instructions from the service provider to setup and login their service.

Move attachments by ZotMoov plugin

You can setup a folder synchronized with online services (OneDrive, Google Drive, DropBox, and Koofr, etc) and use ZotMoov to automatically move Zotero attachments into that folder.

Assuming that folder is D:\obsidian\pdf (Yes, I put it inside my obsidian vault)

In Zotero settings

  • Sync => File Syncing, disable sync attachment files in My Library.
  • Advanced => Files and Folders => Linked attachment base directory => Choose D:\obsidian\pdf.
  • Zotmoov => Directory to Move/Copy files to => Choose D:\obsidian\pdf.

Zotero plugins

https://www.zotero.org/support/plugins

  • Better BibTex : auto generates stable citation keys without clashes.
  • Better Notes: note taking, annotating, exporting, and synchronization. (Optional, as I use Obsidian to take notes)
  • ZotMoov: a simple plugin for managing attachments in Zotero 7. It provides workaround for space limitations (300MB) of online attachment.

Zotero and Obsidian collaboration

Source: Mariana Montes’ post

Zotero side

  • Install Better BibTex plugin.
  • Define a citation key template in Zotero Preferences => Better BibTeX

Obsidian side

  • Install Obsidian
  • Install Zotero integration plugin
  • Setup a Obsidian template for literature notes. I save the following text to _templates/Zotero integration template.md.
---
year: '{{date | format("YYYY")}}'
tags:
citekey: "{{citekey}}"
authors: "{{authors}}"
DOI: "{{DOI}}"
url: "{{url}}"
Zotero link: "{{desktopURI}}"
Journal: "{{journalAbbreviation}}"
Created: 2025-08-10, 15:34:47
Modified: 2025-10-04, 20:48:00
---

# {{title | escape}}

> [!Abstract]-
> {% if abstractNote %}
> {{abstractNote}}
> {% endif %}

> [!Cite]-
> {{bibliography}}

> [!note] PDF link
> {{pdfZoteroLink}}

## Persistent Notes

{% persist "notes" %}{% if isFirstImport %}
`Write your note here.`
{% endif %}{% endpersist %}

## In-text annotations

{% for annotation in annotations -%}
{%- if annotation.annotatedText -%}
{{annotation.annotatedText | safe}}
{%- endif -%}
{% if annotation.comment %}
{{annotation.comment | safe}}
{% endif %}

>  [Page {{annotation.pageLabel}}](zotero://open-pdf/library/items/{{annotation.attachment.itemKey}}?page={{annotation.pageLabel}}&annotation={{annotation.id}})

{% if annotation.imageRelativePath %}
![[{{annotation.imageRelativePath}}]]{% endif %}
{% endfor -%}
  • In the obsidian settings => Zotero integration, setup import formats as follows

And you can use Ctrl+P commands => Zotero integration: Literature note to import paper information into obsidian vault.

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