Zotero Setup Guide

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Overview

• Centralized reference management
• PDF annotation and extraction
• Seamless integration with Obsidian for notes
• Cloud-independent attachment syncing
• Direct API access for AI tools

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Step 1: Install Zotero 7

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1.1 Download Zotero

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1.2 Create Zotero Account

1. Sign up at zotero.org/user/register
2. Sign in to Zotero desktop app
3. Enable sync (File → Preferences → Sync)
   • Note: Free tier includes 300MB storage
   • We’ll set up unlimited attachment storage below

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Step 2: Essential Plugins for Zotero

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2.1 Install Plugin Market (Zotero Addons)

1. Download from: GitHub - Zotero Addons
2. In Zotero: Tools → Add-ons → Install Add-on From File
3. Select the downloaded .xpi file
4. Restart Zotero
5. Access via: Tools → Zotero Addons Manager

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2.2 Better BibTeX (Required)

1. Open Zotero Addons Manager
2. Search “Better BibTeX”
3. Click Install

1. Download from: retorque.re/zotero-better-bibtex
2. Tools → Add-ons → Install Add-on From File

1. Edit → Preferences → Better BibTeX
2. Citation keys (this is my personal preference - totally optional but recommended):
   • Pattern: [auth:lower][year]
   • Example: smith2024
   • Note on duplicates: If you have multiple papers from the same first author in the same year, Better BibTeX automatically adds letters (a, b, c, d) to the end:
     • First paper: smith2024a
     • Second paper: smith2024b
     • Third paper: smith2024c
   • This keeps citation keys unique and memorable!
3. Enable: “On item change, export to” (for auto-export)

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2.3 Attanger - Attachment Management

1. Via Addon Manager: Search “Attanger”
2. Or download from: GitHub - Zotero Attanger

1. Edit → Preferences → Attanger
2. Set custom attachment location:
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   /Users/[username]/Dropbox/Zotero-Attachments/
   or
   /Users/[username]/OneDrive/Zotero-Attachments/
   

3. Enable: “Automatically rename attachments”
4. Rename format (this is my personal preference - works great for searching):
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   {{ citationKey suffix="_" }}{{ title truncate="100" }}
   

   • Creates: smith2024a_Systematic_Review_of_AI_in_Research.pdf
   • Why this format? The citation key makes it easy to remember and find PDFs. The title makes files searchable on your computer. You can easily match PDFs to their Zotero entries!
   • For more format options, see: Zotero File Renaming Guide

• Unlimited storage via your cloud service
• Organized, searchable PDF structure
• Easy to find files by citation key or title
• Access PDFs from any device

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2.4 ZotLit Plugin for Zotero and Obsidian

1. Via Addon Manager: Search for “ZotLit”
2. Or download from: GitHub - ZotLit Releases
3. Install the .xpi file and restart Zotero.

1. In Obsidian, go to Settings > Community Plugins.
2. Turn off “Safe mode”.
3. Browse community plugins and search for “ZotLit”.
4. Install and then enable the plugin.

1. In Obsidian’s ZotLit settings:
   • Connect to the Zotero database. The plugin will usually find the database automatically.
   • Configure the template for your literature notes. A good starting point for the template is provided in the ZotLit documentation.
   • Set the folder where you want your literature notes to be created (e.g., 01-Literature-Notes/).

• From Obsidian, open the command palette (Cmd/Ctrl+P) and search for “ZotLit”.
• You can create new literature notes, insert citations, and pull annotations directly from Zotero into your Obsidian notes.

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Step 3: Enable API Access

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3.1 Zotero MCP Server for Cherry Studio

• Python 3.10+ installed on your system.
• Zotero running.
• Better BibTeX for Zotero plugin installed.

1. In Zotero, go to Edit → Preferences → Advanced → General.
2. Check the box for “Allow other applications to communicate with Zotero”.
3. Note the port number (usually 23119).

1. Install via Smithery (Recommended):
   • Open your terminal and run the following command:
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   npx -y @smithery/cli install @54yyyu/zotero-mcp
   

2. Initial Setup & Embedding Configuration:
   • After installation, run the interactive setup command:
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   zotero-mcp setup
   

   • This process will ask you to choose a semantic search embedding model. You have several options, including:
     • Default: A local model that requires no API keys.
     • Gemini: Uses Google’s embedding models. You will be prompted to enter your Gemini API key.
     • OpenAI: Uses OpenAI’s embedding models. You would need an OpenAI API key.
   • Select Gemini and provide your API key when prompted to enable semantic search on your research library.
3. Build the Database:
   • To allow the MCP to search your Zotero library, you need to build its database. For the most comprehensive search, include full-text extraction:
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   zotero-mcp update-db --fulltext
   

1. In Cherry Studio, go to Settings > MCP Servers > Edit MCP Configuration.
2. Add the following JSON configuration:
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   {
     "mcpServers": {
       "zotero": {
         "name": "zotero",
         "type": "stdio",
         "isActive": true,
         "command": "zotero-mcp",
         "args": [],
         "env": {
           "ZOTERO_LOCAL": "true"
         }
       }
     }
   }
   

• For a general overview, see the developer’s blog post: https://stevenyuyy.us/zotero-mcp/
• For more advanced configuration and troubleshooting, refer to the official GitHub repository: https://github.com/54yyyu/zotero-mcp

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3.2 Better BibTeX API

1. Edit → Preferences → Better BibTeX → API
2. Enable: “Enable BetterBibTeX JSON-RPC”
3. This allows advanced queries from Obsidian

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Step 4: Research Rabbit Integration

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4.1 Prerequisites

1. ✅ Zotero web sync enabled (Edit → Preferences → Sync → logged in)
2. ✅ At least one collection with seed papers
3. ✅ Research Rabbit account created at researchrabbit.ai

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4.2 Connect Research Rabbit to Zotero

1. In Zotero desktop: Edit → Preferences → Sync
2. Log in with your Zotero account
3. Ensure “Sync automatically” is checked
4. Allow sync to complete before proceeding

1. Log into your Research Rabbit account
2. Click “Import Zotero Collection”
3. Sign in with your Zotero credentials when prompted
4. Select the collection you want to import (e.g., “Seed Papers”)
5. Assign a meaningful name in Research Rabbit
6. Click “OK” and wait for import to complete

• Check that all papers imported correctly
• Match imported papers with their titles
• Note: Large collections may import partially

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4.3 Bi-Directional Sync Workflow

1. Create a dedicated collection in Zotero with seed papers
2. Import this collection to Research Rabbit (as above)
3. Use Research Rabbit’s citation network to discover related papers
4. Use the “Similar Papers” and “Citation Map” features

1. In Research Rabbit, build your expanded collection
2. Click “Sync to Zotero” button at the bottom of the page
3. This creates/updates a collection in Zotero
4. New papers will appear in your Zotero library

• After adding papers to either platform: Click “Re-sync with Zotero”
• This ensures both collections stay synchronized

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4.4 Best Practices for Integration

Zotero Collections:
├── Research-2025_SeedPapers          # Original seed papers
├── Research-2025_RR_Discovered       # Papers found via Research Rabbit
└── Research-2025_Final_Curated       # Final selection after human review

1. Start in Zotero: Import 3-5 seed papers from databases
2. Explore in Research Rabbit: Import seed collection, discover related papers
3. Curate in Zotero: Sync discoveries back, apply inclusion criteria
4. Iterate: Repeat discovery-curation cycles as needed

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4.5 Troubleshooting Integration

• Ensure Zotero web sync is active and up-to-date
• Try logging out/in of Research Rabbit
• Check if you’re using a group library (may cause issues)
• Use personal library collections only

• Large collections may not import completely
• Break into smaller sub-collections (<50 papers)
• Use BibTeX export/import as fallback:
  1. In Research Rabbit: Export → BibTeX
  2. In Zotero: File → Import → select .bib file

• Research Rabbit may only sync with personal libraries
• Create personal collections for Research Rabbit integration
• Copy papers from group library to personal library if needed

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4.6 Alternative Export Methods

1. Click “Export” in left sidebar
2. Choose BibTeX (.bib) format
3. Download file

1. File → Import
2. Select the .bib file
3. Choose “Place imported items in new collection”
4. Name collection appropriately

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Step 5: Configure for Systematic Reviews

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5.1 Create Collections Structure

My Library/
├── Systematic Review Project/
│   ├── Search Results/
│   │   ├── Database 1/
│   │   ├── Database 2/
│   │   └── Grey Literature/
│   ├── Screening/
│   │   ├── Title-Abstract/
│   │   ├── Full-Text/
│   │   └── Excluded/
│   ├── Included Studies/
│   └── Analysis/

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5.2 Set Up Tags for Review Stages

• #to-screen
• #screening-passed
• #full-text-review
• #included
• #excluded-reason-1 (not relevant)
• #excluded-reason-2 (wrong methodology)
• #excluded-reason-3 (duplicate)

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5.3 Create Saved Searches

1. Edit → New Saved Search
2. Examples:
   • “Needs Screening”: Tag is not #screening-passed
   • “Recent AI Papers”: Date Added in last 7 days AND Any field contains “AI”
   • “High Quality”: Item Type is “Journal Article” AND Publication contains “Nature” OR “Science”

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Step 6: Import and Export Settings

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6.1 Import from Databases

• Web of Science: BibTeX or RIS
• Scopus: RIS or BibTeX
• PubMed: PubMed XML
• IEEE Xplore: BibTeX
• Google Scholar: Use Zotero Connector

1. File → Import
2. Choose file format
3. Select: “Place imported items in new collection”
4. Name: “Database Name - Date”

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6.2 Export for Analysis

• Better BibTeX → Export Library
• Format: Better CSL JSON or Better BibTeX
• Keep updated: Check this for auto-sync

• Use API access (configured above)
• Or export as CSL JSON

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Step 7: PDF Management and Annotation

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7.1 Built-in PDF Reader

1. Double-click any PDF
2. Use highlighting tools (colors can have meaning!)
   • Yellow: Important points
   • Red: Disagree/Question
   • Green: Agree/Support
   • Blue: Methodology
   • Purple: Future research

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7.2 Extract Annotations

1. Right-click PDF → “Add Note from Annotations”
2. Creates structured note with:
   • All highlights with page numbers
   • Your comments
   • Links back to PDF location

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7.3 Export Annotations to Obsidian

1. Right-click → “Create Obsidian Note”
2. Annotations automatically included
3. Each highlight links back to PDF page

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Step 8: Backup Strategy

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8.1 Database Backup

• Windows: C:\Users\[username]\Zotero
• Mac: /Users/[username]/Zotero
• Linux: /home/[username]/Zotero

• External drive
• Cloud service (different from attachment sync)

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8.2 Export Library Backup

1. File → Export Library
2. Format: Zotero RDF (includes most metadata)
3. Include: Files and Notes
4. Save with date: Zotero-Backup-2025-09-01.rdf

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Troubleshooting

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Common Issues

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Sync Conflicts

• Disable auto-sync during bulk imports
• Resolve conflicts by choosing “Use local version”
• Re-enable after import complete

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Attachment Not Found

• Check Attanger settings
• Verify cloud folder is synced
• Tools → Manage Attachments → Convert to Linked Files

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Better BibTeX Slow

• Reduce citation key update frequency
• Disable “Background export”
• Pin citation keys for large libraries

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API Not Working

• Check firewall settings
• Restart Zotero
• Verify port 23119 is not in use

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Plugin Compatibility

• Always check “Compatible with Zotero”
• Disable old plugins before updating
• Check GitHub issues for known problems

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Quick Reference

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Keyboard Shortcuts

• Cmd/Ctrl + Shift + N: New item from identifier (DOI, ISBN)
• Cmd/Ctrl + Shift + A: Add attachment
• Cmd/Ctrl + Shift + C: Copy citation
• Tab: Move between fields
• Shift + Enter: Create new creator field

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Useful Workflows

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Adding Papers from PDF

1. Drag PDF into Zotero
2. Right-click → “Retrieve Metadata for PDF”
3. Verify and correct metadata
4. Add tags for review stage

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Bulk Tagging

1. Select multiple items
2. Drag to tag in left panel
3. Or right-click → “Assign Tags”

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Quick Export to Obsidian

1. Select papers
2. Cmd/Ctrl + Shift + C (with Better BibTeX)
3. Paste in Obsidian with citations

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Integration Points

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With Obsidian

• Better BibTeX provides citation keys
• Obsidian Note plugin creates notes
• Annotations sync automatically

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With Cherry Studio

• Local API enables MCP access
• Zotero MCP searches library
• Exports feed AI knowledge base

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With Cloud Services

• Attanger manages PDF sync
• Independent of Zotero storage
• Works with any cloud provider

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Checklist

• Install Zotero
• Install all essential plugins
• Configure Better BibTeX citation keys
• Set up Attanger with cloud folder
• Enable local API access
• Create Research Rabbit account
• Test Research Rabbit-Zotero sync with seed papers
• Create collections structure
• Import 3-5 seed papers
• Test Obsidian Note creation
• Verify API at http://localhost:23119

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Resources

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Integration with Other Tools

• Complete your research pipeline: Research Rabbit Setup Guide for paper discovery
• Set up AI analysis: Cherry Studio Setup Guide for working with your collections via the Zotero MCP server
• Understand model options: AI Model Reference Guide
• Learn quality control: Failure Museum

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External Support Resources

• Zotero Forums
• Better BibTeX Documentation
• Zotero Plugins Directory