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OpenBio integrates with Zotero, the popular reference management system, allowing you to search, manage, and cite your research library directly within your research conversations. Access your citations, collections, and notes without leaving OpenBio.
What is Zotero?Zotero is a free, open-source reference management tool that helps you collect, organize, cite, and share research sources. OpenBio’s Zotero integration lets you access your Zotero library directly from your research conversations.
Watch a demo of Zotero integration in action:

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Overview

With Zotero integration, you can:
  • Search your library: Find papers, books, and other references
  • Manage collections: Organize references into collections
  • Access metadata: View titles, authors, abstracts, and more
  • Create citations: Add new references to your library
  • Download attachments: Access PDFs and files from Zotero
  • Manage notes: Create and search notes linked to references

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Setting Up Zotero

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Connecting Your Account

Location: Profile Settings → Zotero Settings tab
1

Open Zotero Settings

Navigate to Profile → Settings → Zotero Settings
2

Connect with Zotero

Click the “Connect with Zotero” button
3

Authorize Access

You’ll be redirected to Zotero to authorize OpenBio
  • Log in to your Zotero account
  • Review permissions requested
  • Click “Authorize” to grant access
4

Verify Connection

Return to OpenBio settings
  • Status should show “Connected”
  • Your Zotero user ID and display name appear
  • Last verified timestamp is shown

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Connection Status

The Zotero settings page shows:
  • Connection status: Connected, configured but not verified, or not connected
  • User information: Your Zotero user ID and display name
  • Last verified: When the connection was last checked
  • Library access: Which libraries are available

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Disconnecting

To remove Zotero integration:
  1. Click “Disconnect” button
  2. Confirm disconnection
  3. Zotero tools will no longer be available

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Reconnecting

If your connection expires or needs refreshing:
  1. Click “Disconnect” button
  2. Complete the authorization flow again
  3. Your connection is restored

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Using Zotero in Chat

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Searching Your Library

Ask OpenBio to search your Zotero library: 
Search my Zotero library for papers about CRISPR
Find references related to protein folding
Show me recent items added to Zotero

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Accessing Collections

Work with your Zotero collections: 
Show me items in my "CRISPR Research" collection
List all collections in my library
Get items from the top-level collection "Biology"

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Creating References

Add new items to your library: 
Add this paper to my Zotero library:
Title: "Novel Protein Design Methods"
Authors: Smith, J. and Jones, M.
Year: 2024

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Managing Items

Update and organize references: 
Update the tags on the paper about kinase inhibitors
Add a note to the CRISPR paper about key findings
Delete the duplicate entry for the protein structure paper

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Zotero Features Available

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Search and Discovery

  • Quick search: Search across titles, authors, and abstracts
  • Advanced search: Filter by item type, tags, collections
  • Recent items: View recently added references
  • Item type filtering: Find specific types (journal articles, books, etc.)

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Collection Management

  • View collections: Browse your collection hierarchy
  • Collection items: See items in specific collections
  • Create collections: Organize references into new collections
  • Update collections: Modify collection names and structure

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Item Operations

  • View details: See full metadata for any reference
  • Create items: Add new references manually
  • Update items: Modify existing reference information
  • Delete items: Remove references from your library
  • Batch operations: Perform actions on multiple items

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Notes and Tags

  • Create notes: Add standalone or item-linked notes
  • Search notes: Find notes by content
  • Manage tags: Add, remove, and search tags
  • Tag filtering: Filter items by tags

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File Attachments

  • View attachments: See files attached to references
  • Download files: Access PDFs and other attachments
  • Create attachments: Add files to references
  • Update files: Replace or modify attachment files

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Common Use Cases

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Literature Review

1. Search Zotero: "Find all papers about protein design from 2023"
2. Review results and identify key papers
3. Create a collection: "Protein Design Review"
4. Add selected papers to the collection
5. Create notes summarizing key findings

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Citation Management

1. Ask: "Add this paper to Zotero: [paper details]"
2. OpenBio creates the reference with metadata
3. Add to relevant collection
4. Attach PDF if available
5. Tag with relevant keywords

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Research Organization

1. Search library for specific topic
2. Review items and organize into collections
3. Add tags for easy filtering
4. Create notes with key insights
5. Export bibliography for papers

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Best Practices

Use collections and tags consistently to make searching easier.
When creating items, include as much information as possible (DOI, abstract, keywords).
Tag items with relevant keywords for easy filtering and discovery.
Add notes to important papers with key findings and your thoughts.
Keep your Zotero library synced to ensure OpenBio has the latest references.

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Troubleshooting

Solutions:
  • Click “Reconnect with Zotero”
  • Verify Zotero account credentials
  • Check internet connection
  • Try disconnecting and reconnecting
Solutions:
  • Ensure Zotero sync is enabled in Zotero desktop app
  • Wait a few minutes for sync to complete
  • Try refreshing the connection in OpenBio

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Library Permissions

Zotero supports different library types with varying permissions:

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Personal Libraries

  • Full access: Read, write, files, notes
  • Your library: Complete control over all operations

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Group Libraries

Permissions depend on your role:
  • Owner/Admin: Full access
  • Member (write): Can create/edit items and collections
  • Member (read): Can view items but not modify
  • Member (files): Can access file attachments
Some operations may be limited based on your permissions in group libraries. OpenBio will show helpful error messages if an operation isn’t allowed.

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Integration with Research Workflow

  1. Search PubMed or other databases in OpenBio
  2. Add interesting papers directly to Zotero
  3. Organize into collections
  4. Create notes with key findings

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While Writing

  1. Search Zotero for relevant citations
  2. Get formatted citations
  3. Export bibliography
  4. Access PDFs directly

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For Project Organization

  1. Create collections per research project
  2. Tag items with project identifiers
  3. Add notes linking to OpenBio analyses
  4. Track research progress

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Next Steps

Chat Guide

Learn how to use Zotero tools in conversations

Profile Settings

Manage your Zotero connection

Tools Reference

Explore all available tools

Notebooks

Document your research findings
Pro Tip: Keep your Zotero library well-organized with collections and tags. This makes it much easier to find relevant papers when you need them during your research conversations!